Contacts of the helix formed by residues 123 - 139 (chain A) in PDB entry 4LOU
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 ARG 123 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A TYR 3.8 11.1 + - - -
101A ALA* 4.4 3.2 - - - +
102A PRO* 4.5 6.9 - - - +
103A GLU* 3.1 45.3 + - - +
121A PRO* 3.4 28.7 + - + +
122A VAL* 1.3 69.4 - - - +
124A TRP* 1.3 57.3 + - - +
125A TRP* 3.2 31.8 - - + +
126A ARG* 3.0 38.7 + - + +
127A VAL* 2.9 26.1 + - + +
157A ASN* 3.7 5.3 + - - -
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Residues in contact with TRP 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A VAL 2.7 18.3 + - - +
123A ARG* 1.3 73.1 - - - +
125A TRP* 1.3 90.5 + + + +
126A ARG 3.4 0.2 + - - -
127A VAL 4.0 0.7 - - - +
128A LEU* 3.3 27.4 + - + +
129A PRO* 4.2 0.2 - - - +
157A ASN* 3.4 36.8 - - + +
160A ARG* 3.8 7.2 - - + -
161A MET* 3.5 50.6 - - + +
164A ASP* 2.7 37.8 + - + -
165A ILE* 5.2 9.0 - - + -
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Residues in contact with TRP 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PRO* 6.5 0.4 - - + -
122A VAL 3.9 4.0 - - - -
123A ARG* 3.8 32.6 - - + +
124A TRP* 1.3 130.5 - + + +
126A ARG* 1.3 98.3 + - + +
129A PRO* 3.5 17.3 - - - +
164A ASP* 4.5 4.5 - - - -
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Residues in contact with ARG 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LYS 4.7 1.6 + - - -
100A TYR* 2.6 63.5 + - + +
101A ALA* 4.3 4.7 - - + -
123A ARG* 3.0 35.3 + - + +
125A TRP* 1.3 107.3 - - + +
127A VAL* 1.3 59.1 + - - +
128A LEU 3.6 0.7 - - - -
129A PRO* 3.3 5.1 - - - +
130A VAL* 3.1 35.0 + - + +
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Residues in contact with VAL 127 (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 ALA* 4.4 4.0 - - + -
103A GLU* 3.3 37.5 - - + +
104A ALA* 4.0 18.4 - - + -
123A ARG* 2.9 14.7 + - + +
126A ARG* 1.3 76.1 - - - +
128A LEU* 1.3 61.1 + - + +
130A VAL* 4.5 4.3 - - - +
131A LYS* 2.7 37.9 + - + +
153A GLN* 4.1 16.8 - - + +
154A ILE* 5.5 0.7 - - - +
157A ASN* 3.3 33.9 - - + +
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Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A TRP* 3.3 21.6 + - + +
127A VAL* 1.3 80.7 - - - +
129A PRO* 1.4 71.4 - - + +
131A LYS* 4.3 0.6 - - - +
132A PHE* 3.1 24.4 + - - +
154A ILE* 3.5 38.5 - - + +
157A ASN* 3.7 13.7 - - + -
158A ILE* 3.6 19.1 - - + -
161A MET* 3.9 31.6 - - + -
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Residues in contact with PRO 129 (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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96A LEU* 4.7 2.4 - - + +
124A TRP 4.2 0.2 - - - +
125A TRP 3.5 20.9 - - - +
126A ARG* 3.3 11.4 - - - +
128A LEU* 1.4 92.4 - - + +
130A VAL* 1.3 67.4 + - + +
132A PHE* 4.6 0.7 - - + -
133A PHE* 3.1 47.6 + - + +
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Residues in contact with VAL 130 (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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96A LEU* 3.1 42.8 - - + +
97A VAL* 3.7 24.6 - - + +
100A TYR* 3.7 21.8 - - + -
101A ALA* 3.7 16.4 - - + -
104A ALA* 4.0 4.5 - - + -
126A ARG* 3.1 20.6 + - - +
127A VAL* 4.1 1.1 - - - +
129A PRO* 1.3 80.1 - - + +
131A LYS* 1.3 55.1 + - - +
134A GLY* 2.6 37.1 + - - -
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Residues in contact with LYS 131 (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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53A PHE* 4.2 2.6 - - - -
104A ALA* 3.1 27.9 + - + +
105A GLY 3.3 4.0 + - - -
106A GLY 2.9 27.1 + - - -
107A SER 3.2 16.4 + - - -
127A VAL* 2.7 27.6 + - + +
130A VAL* 1.3 76.2 - - - +
132A PHE* 1.3 54.0 + - - +
134A GLY* 5.1 0.2 - - - -
135A GLY* 2.8 32.4 + - - +
149A GLY 4.3 1.1 - - - -
150A PRO* 3.8 24.8 - - + +
153A GLN* 2.7 30.4 + - + +
154A ILE* 3.8 24.7 - - + -
353A PRO* 4.7 8.8 - - + +
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Residues in contact with PHE 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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49A ALA* 4.0 14.1 - - + -
52A ALA* 4.2 14.1 - - + -
53A PHE* 3.6 49.4 - + + -
128A LEU 3.1 19.0 + - - +
129A PRO* 4.0 2.0 - - + +
131A LYS* 1.3 78.9 - - - +
133A PHE* 1.3 84.4 + + + +
136A LEU* 3.0 52.2 + - + +
154A ILE* 3.9 19.4 - - + +
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Residues in contact with PHE 133 (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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92A PHE* 3.8 27.2 - + + -
96A LEU* 4.3 14.1 - - + -
129A PRO* 3.1 41.4 + - + +
132A PHE* 1.3 95.0 - + - +
134A GLY* 1.3 65.0 + - - +
135A GLY 3.1 1.8 - - - -
136A LEU* 3.4 16.3 + - + +
137A GLY* 3.4 14.7 + - - -
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Residues in contact with GLY 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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93A GLY* 3.5 31.8 - - - -
96A LEU* 4.5 6.6 - - - +
130A VAL* 2.6 24.3 + - - -
133A PHE* 1.3 73.9 - - - +
135A GLY* 1.3 58.7 + - - +
137A GLY 3.4 7.3 + - - -
138A THR 3.4 7.6 + - - -
353A PRO* 3.1 21.9 - - - +
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Residues in contact with GLY 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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53A PHE* 4.1 16.2 - - - -
131A LYS 2.8 20.6 + - - -
132A PHE 3.9 0.7 - - - -
134A GLY* 1.3 73.6 - - - +
136A LEU* 1.3 52.3 + - - +
137A GLY 2.7 15.5 + - - -
138A THR* 3.1 7.0 + - - -
139A LEU* 2.9 30.5 + - - +
150A PRO* 5.3 2.9 - - - -
353A PRO* 3.9 10.0 - - - +
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Residues in contact with LEU 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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53A PHE* 3.8 11.5 - - + +
56A GLY* 3.5 15.3 - - - +
57A VAL* 3.3 42.8 - - + +
60A LEU* 3.2 31.1 - - + +
89A LEU* 4.9 1.2 - - - +
132A PHE* 3.0 48.6 + - + +
133A PHE* 3.6 20.9 - - + +
135A GLY* 1.3 72.1 - - - +
137A GLY* 1.3 59.3 + - - +
140A GLY* 3.5 11.9 + - - -
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Residues in contact with GLY 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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89A LEU* 3.3 44.7 - - - +
90A ALA 4.0 0.3 + - - -
92A PHE* 5.0 3.8 - - - -
93A GLY* 5.0 1.3 - - - -
133A PHE 3.4 9.3 + - - -
134A GLY 3.4 4.7 + - - -
135A GLY 2.7 4.0 + - - -
136A LEU* 1.3 79.9 - - - +
138A THR* 1.3 58.3 + - - -
141A GLY* 3.0 22.7 + - - -
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Residues in contact with THR 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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90A ALA* 4.1 19.1 - - - +
94A TYR* 4.4 2.0 - - + +
134A GLY 3.4 8.5 + - - +
135A GLY 3.2 7.3 + - - -
137A GLY* 1.3 76.2 - - - +
139A LEU* 1.3 62.8 + - - +
141A GLY* 3.6 0.7 + - - -
142A GLY 3.5 2.8 + - - -
143A MET* 3.0 57.9 + - - +
145A LEU* 4.2 4.7 - - - -
352A ALA* 3.9 5.4 - - + -
353A PRO* 2.8 48.5 + - + +
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Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PHE* 3.8 19.5 - - + -
57A VAL* 3.7 15.9 - - + -
61A GLN* 2.8 16.9 + - - +
135A GLY 2.9 16.3 + - - +
138A THR* 1.3 84.2 + - - +
140A GLY* 1.3 56.5 + - - +
141A GLY 3.0 4.7 - - - -
142A GLY* 2.8 22.2 + - - -
143A MET 4.0 3.8 + - - +
145A LEU* 3.6 44.0 - - + +
146A GLY* 3.3 27.1 - - - +
147A ARG* 3.6 21.8 - - + +
150A PRO* 4.3 3.4 - - + -
353A PRO 4.3 4.7 - - - +
354A GLY* 4.5 0.7 - - - -
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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