Contacts of the helix formed by residues 127 - 148 (chain A) in PDB entry 4KPD
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 127 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ARG* 3.8 18.8 + - - +
123A GLY 4.5 6.9 - - - +
124A VAL 3.3 15.8 - - - +
125A GLY 3.1 1.4 - - - -
126A LEU* 1.4 76.5 - - - +
128A ALA* 1.3 61.1 + - - +
130A ASN* 3.0 20.8 + - - +
131A ASP* 3.3 13.6 + - - +
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Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A VAL* 3.6 6.3 - - + +
105A ILE* 3.9 9.6 - - + -
118A TRP* 3.7 21.3 - - + -
119A TYR* 3.7 17.7 - - + -
124A VAL* 3.9 3.6 - - + +
125A GLY 3.2 17.5 + - - +
126A LEU 3.0 0.2 - - - -
127A ASP* 1.3 74.4 - - - +
129A ILE* 1.4 58.6 + - - +
130A ASN 3.4 0.2 - - - -
131A ASP* 3.4 15.9 + - - +
132A ALA* 2.8 31.4 + - - +
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Residues in contact with ILE 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ALA* 6.3 0.9 - - - -
105A ILE* 3.9 21.1 - - + +
126A LEU* 3.1 35.4 + - + +
127A ASP 3.1 0.8 - - - -
128A ALA* 1.4 79.3 - - - +
130A ASN* 1.3 61.4 + - - +
132A ALA* 3.3 7.2 + - - +
133A ASN* 3.2 34.6 + - - +
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Residues in contact with ASN 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU 4.6 0.2 + - - -
127A ASP* 3.0 11.0 + - - +
129A ILE* 1.3 75.6 - - - +
131A ASP* 1.3 61.0 + - - +
133A ASN* 3.2 15.7 + - - +
134A LEU* 3.0 41.5 + - - +
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Residues in contact with ASP 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ARG* 2.9 38.3 + - - +
48A VAL* 3.5 25.2 - - + +
101A VAL* 5.2 0.9 - - + -
118A TRP* 2.7 32.2 + - + +
127A ASP* 3.3 7.5 + - - +
128A ALA* 3.4 13.7 - - - +
130A ASN* 1.3 80.1 + - - +
132A ALA* 1.4 61.4 + - - +
134A LEU* 3.2 15.8 + - - +
135A LEU* 3.1 24.9 + - - +
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Residues in contact with ALA 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A PHE* 3.2 41.6 - - + +
101A VAL* 3.9 13.0 - - + +
102A ALA* 4.4 10.5 - - + +
128A ALA 2.8 17.4 + - - +
129A ILE* 3.4 8.5 - - - +
130A ASN 3.3 0.2 - - - -
131A ASP* 1.4 75.9 - - - +
133A ASN* 1.4 61.8 + - - +
135A LEU* 3.1 24.8 + - - +
136A GLU 3.2 4.5 + - - -
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Residues in contact with ASN 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PHE* 3.9 16.0 - - - -
129A ILE* 3.2 30.5 + - - +
130A ASN* 3.2 16.9 + - - +
132A ALA* 1.4 75.6 - - - +
134A LEU* 1.4 56.9 + - - +
136A GLU* 3.3 18.2 + - - +
137A ALA* 2.9 27.6 + - - +
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Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ALA* 5.1 5.6 - - + +
44A ARG* 5.6 3.4 - - + -
45A LEU* 4.1 39.7 - - + +
48A VAL* 5.4 2.9 - - + -
130A ASN* 3.0 27.3 + - - +
131A ASP* 3.2 22.6 + - - +
133A ASN* 1.4 73.7 - - - +
135A LEU* 1.4 57.4 - - - +
137A ALA* 3.2 12.3 + - + +
138A CYS* 3.0 35.1 + - - -
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Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU* 5.6 0.9 - - + -
48A VAL* 3.8 26.7 - - + +
49A LEU* 3.8 34.1 - - + -
52A ASN* 4.1 4.7 - - + -
53A ALA* 5.2 1.1 - - + -
94A LEU* 3.8 31.5 - - + +
97A ALA* 3.8 38.8 - - + +
98A PHE 4.1 2.2 - - - +
101A VAL* 4.0 14.6 - - + -
131A ASP 3.1 12.9 + - - +
132A ALA* 3.1 12.4 + - - +
134A LEU* 1.4 72.1 - - - +
136A GLU* 1.3 65.1 + - - +
138A CYS* 3.3 18.7 + - - +
139A ILE* 3.7 4.2 + - - +
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Residues in contact with GLU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A LEU* 5.0 2.5 - - + -
98A PHE* 3.7 52.1 - - + +
132A ALA 3.2 2.4 + - - -
133A ASN* 3.3 18.1 + - - +
135A LEU* 1.3 78.3 - - - +
137A ALA* 1.4 61.6 + - - +
139A ILE* 3.2 33.3 + - + +
140A TYR* 3.5 22.4 + - + -
161A LEU* 5.9 1.7 - - - +
164A SER* 4.4 13.2 + - - +
168A GLU* 4.5 2.4 - - - +
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Residues in contact with ALA 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ASN 2.9 15.0 + - - +
134A LEU* 3.2 19.7 + - + +
136A GLU* 1.4 75.6 - - - +
138A CYS* 1.4 60.2 + - - +
139A ILE 3.3 0.9 + - - -
140A TYR* 3.3 17.3 + - - +
141A ARG* 3.4 21.2 + - + +
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Residues in contact with CYS 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 3.8 30.7 - - + -
45A LEU* 3.7 35.9 - - - -
49A LEU* 4.6 5.4 - - + -
94A LEU* 3.9 9.0 - - + -
134A LEU* 3.0 19.9 + - - -
135A LEU* 3.6 9.9 - - - +
136A GLU 3.3 0.6 - - - -
137A ALA* 1.4 72.4 - - - +
139A ILE* 1.4 63.5 + - - +
140A TYR 3.4 0.2 - - - -
141A ARG* 3.4 13.1 + - - +
142A LEU* 3.1 28.2 + - - +
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Residues in contact with ILE 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A CYS* 3.4 35.7 - - + +
94A LEU* 3.8 12.7 - - + +
95A LEU* 3.7 44.9 - - + +
135A LEU 3.7 1.0 + - - +
136A GLU* 3.2 25.7 + - + +
138A CYS* 1.4 76.7 - - - +
140A TYR* 1.3 70.2 + - + +
142A LEU 3.4 1.6 + - - -
143A LEU* 3.0 35.5 + - + +
160A PHE* 3.7 29.4 - - + -
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Residues in contact with TYR 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A LEU* 5.5 0.3 - - - +
136A GLU* 3.5 34.9 + - + -
137A ALA* 3.3 9.1 + - - +
139A ILE* 1.3 83.3 - - + +
141A ARG* 1.3 59.2 + - - +
142A LEU 3.4 0.2 - - - -
143A LEU* 3.9 15.5 - - + +
144A LYS* 3.1 29.3 + - - +
153A TYR* 4.9 1.4 + - - -
157A ILE* 4.0 26.5 - - + -
160A PHE* 3.4 44.9 + - + +
161A LEU* 3.4 24.7 - - + +
164A SER* 4.0 6.1 + - - -
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Residues in contact with ARG 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL 4.1 6.5 + - - -
28A LEU* 2.9 55.8 + - + +
30A GLU 5.6 1.8 - - - +
42A ILE* 4.8 7.6 - - - +
45A LEU* 4.0 14.8 - - - +
137A ALA* 3.4 19.3 + - + +
138A CYS* 3.5 14.3 - - - +
140A TYR* 1.3 76.7 - - - +
142A LEU* 1.4 57.7 + - - +
144A LYS* 3.5 7.1 + - - +
145A LEU* 3.0 43.7 + - + +
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Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 4.2 34.5 - - + +
27A VAL* 4.6 10.3 - - + -
28A LEU* 3.8 24.9 - - + -
87A THR* 4.0 11.0 - - + +
90A TRP* 5.2 0.4 - - + -
91A CYS* 3.8 21.5 - - - +
94A LEU* 3.8 28.5 - - + -
138A CYS 3.1 14.9 + - - +
141A ARG* 1.4 73.5 - - - +
143A LEU* 1.4 63.4 + - - +
145A LEU* 3.3 3.5 + - + -
146A TYR* 3.0 50.4 + - + +
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Residues in contact with LEU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A THR* 5.9 0.7 - - + -
88A VAL* 4.0 26.5 - - + -
91A CYS* 4.1 12.8 - - - -
139A ILE* 3.0 29.7 + - + +
140A TYR* 3.9 19.7 - - + +
141A ARG 3.4 0.2 - - - -
142A LEU* 1.4 75.0 - - - +
144A LYS* 1.3 56.3 + - - +
147A CYS* 2.8 32.4 + - + -
148A ARG 3.3 6.8 + - - -
153A TYR* 3.3 17.5 - - + -
156A LEU* 4.1 15.9 - - + -
157A ILE* 4.3 20.9 - - + +
160A PHE* 4.0 26.7 - - + -
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Residues in contact with LYS 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A TYR 3.1 19.0 + - - +
141A ARG* 3.7 7.4 - - - +
143A LEU* 1.3 75.1 - - - +
145A LEU* 1.3 63.0 + - + +
146A TYR 3.5 0.2 + - - -
148A ARG* 3.2 43.9 + - + +
153A TYR* 3.6 23.1 + - - +
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Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 3.5 35.2 - - + +
28A LEU* 5.0 2.9 - - + -
141A ARG* 3.0 36.8 + - + +
142A LEU* 3.3 10.3 + - + +
144A LYS* 1.3 79.6 - - + +
146A TYR* 1.3 70.6 + - + +
148A ARG* 3.8 18.0 + - - +
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Residues in contact with TYR 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLN* 4.9 6.6 + - - +
24A ILE* 5.3 4.4 - - + +
27A VAL* 3.3 35.9 - - + +
83A GLN* 3.6 44.7 + - + -
84A ARG* 3.2 32.1 + - + +
86A TRP* 5.6 2.2 - + - -
87A THR* 3.6 28.9 - - + -
142A LEU* 3.0 37.2 + - + +
145A LEU* 1.3 86.3 - - + +
147A CYS* 1.3 65.2 + - - +
148A ARG* 3.8 1.6 - - - -
149A GLU 5.6 0.2 - - - -
150A GLN* 4.5 2.1 + - - +
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Residues in contact with CYS 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ARG* 4.2 15.7 - - - -
87A THR* 5.8 1.1 - - - -
88A VAL* 4.0 26.5 - - - -
143A LEU* 2.8 27.6 + - + +
146A TYR* 1.3 82.6 - - - +
148A ARG* 1.4 63.0 + - - +
149A GLU 3.3 3.4 - - - -
150A GLN* 3.1 20.6 + - - +
152A TYR* 4.1 24.0 - - + -
153A TYR* 3.2 19.7 - - + +
156A LEU* 4.5 6.1 - - + -
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Residues in contact with ARG 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LEU 3.3 3.8 + - - -
144A LYS* 3.2 36.2 + - + +
145A LEU* 3.8 23.0 + - - +
146A TYR 3.8 0.8 - - - -
147A CYS* 1.4 76.2 - - - +
149A GLU* 1.3 83.3 + - + +
150A GLN 3.6 1.6 + - - +
153A TYR* 3.6 35.5 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il