Contacts of the strand formed by residues 121 - 136 (chain A) in PDB entry 4STD
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 VAL 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A GLN* 3.8 19.1 - - + +
112A ARG 3.7 9.2 - - - +
113A TYR* 3.5 26.2 - - + -
120A GLU* 1.3 85.2 - - - +
122A THR* 1.3 61.9 + - - +
123A MET 3.9 4.5 - - - +
124A LYS* 3.9 29.8 - - + -
156C PHE 6.3 0.9 - - - +
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Residues in contact with THR 122 (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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112A ARG* 2.7 17.7 + - - -
113A TYR 3.2 5.7 + - - +
114A LYS* 3.1 49.8 + - + +
120A GLU* 5.5 1.3 - - - -
121A VAL* 1.3 75.0 - - - +
123A MET* 1.3 75.1 + - + +
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Residues in contact with MET 123 (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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110A HIS 4.0 0.2 - - - +
111A GLN* 3.4 3.5 - - - -
112A ARG* 2.8 69.0 + - + +
121A VAL* 3.8 2.3 - - - +
122A THR* 1.3 91.0 - - + +
124A LYS* 1.3 68.3 + - - +
157A ASP* 5.0 7.6 - - + +
160A ARG* 3.5 37.9 - - + +
161A ILE* 4.2 11.2 - - + +
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Residues in contact with LYS 124 (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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110A HIS 3.3 6.7 - - - +
111A GLN* 3.4 24.9 - - + +
121A VAL* 3.9 16.4 - - + -
123A MET* 1.3 80.6 - - - +
125A GLY* 1.3 59.3 + - - +
126A HIS* 4.2 8.5 - - + -
156A PHE* 3.4 38.8 - - + +
157A ASP* 3.0 28.9 + - - +
161A ILE* 3.9 5.2 - - - -
155C GLU* 2.8 34.1 + - + +
156C PHE* 3.7 18.4 - - - +
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Residues in contact with GLY 125 (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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110A HIS* 2.8 42.8 + - - +
124A LYS* 1.3 76.7 - - - +
126A HIS* 1.3 65.5 + - - +
155A GLU 3.5 9.0 - - - -
156A PHE* 4.3 0.2 - - - +
157A ASP 3.6 1.1 - - - -
158A PHE* 3.6 23.5 - - - -
161A ILE* 3.9 4.1 - - - +
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Residues in contact with HIS 126 (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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107A ARG* 3.2 32.8 - - - +
108A VAL 3.2 3.8 - - - +
109A PRO* 3.0 31.6 - - + +
110A HIS 3.3 17.0 + - - -
111A GLN* 5.5 0.7 - - + -
124A LYS* 4.2 10.3 - - + +
125A GLY* 1.3 80.1 - - - -
127A ALA* 1.3 59.5 + - - +
128A HIS* 3.4 6.0 - - + -
154A GLY* 3.1 3.8 - - - -
155A GLU* 2.7 47.7 + - + -
156A PHE* 3.6 24.6 - + - -
158A PHE* 4.3 1.3 - - - +
153C TRP* 5.3 2.0 - + - -
155C GLU* 3.0 30.1 + - + -
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Residues in contact with ALA 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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106A LEU 3.7 0.5 - - - +
107A ARG* 3.2 6.4 - - - +
108A VAL* 2.8 35.9 + - - +
125A GLY 4.0 0.8 + - - -
126A HIS* 1.3 73.2 - - - +
128A HIS* 1.3 62.6 + - - +
129A SER 4.1 0.4 - - - -
151A ILE* 4.0 9.6 - - + -
153A TRP 3.8 3.8 - - - -
154A GLY* 4.3 1.6 - - - -
158A PHE* 3.9 23.7 - - + -
173A BFS 3.1 35.0 - - + -
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Residues in contact with HIS 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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106A LEU 3.4 5.2 - - - -
107A ARG* 3.5 23.1 + - + +
126A HIS 3.4 20.4 + - - -
127A ALA* 1.3 70.7 - - - +
129A SER* 1.3 60.7 + - - +
151A ILE* 3.8 1.2 - - - -
152A ARG* 3.0 25.1 + - + +
153A TRP* 3.0 80.7 + + + +
155A GLU* 3.8 14.9 + - + -
84B GLN* 3.0 40.2 - - + +
109B PRO* 4.1 9.6 - - + +
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Residues in contact with SER 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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105A GLN* 3.6 2.6 - - - -
106A LEU* 2.7 45.4 + - - +
127A ALA 4.1 0.2 - - - -
128A HIS* 1.3 76.1 - - - +
130A ALA* 1.3 58.5 - - - +
131A ASN* 2.8 26.0 + - - -
150A ASP 3.2 17.9 - - - -
151A ILE* 3.4 20.2 - - - -
152A ARG* 4.3 5.4 - - - +
173A BFS 3.3 16.5 - - - -
84B GLN* 3.8 4.1 + - - +
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Residues in contact with ALA 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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104A HIS 3.8 4.3 - - - -
105A GLN* 4.9 1.6 - - - +
129A SER* 1.3 72.3 - - - +
131A ASN* 1.3 62.9 + - - +
132A LEU 3.9 0.3 + - - -
148A LYS 3.8 2.3 - - - +
150A ASP* 3.0 33.5 + - + +
152A ARG* 3.4 38.5 - - - +
24B TYR* 4.3 11.9 - - - +
28B ASP* 3.9 7.6 - - - +
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Residues in contact with ASN 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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26A TRP* 4.0 0.5 - - - -
102A GLY 3.4 4.3 - - - +
103A TYR* 3.4 4.9 - - - -
104A HIS* 2.8 49.8 + - + +
106A LEU* 3.4 17.5 - - + +
129A SER* 2.8 29.9 + - - -
130A ALA* 1.3 72.0 - - - +
132A LEU* 1.3 59.5 + - - +
133A HIS* 3.3 28.1 + - + +
147A LEU* 4.3 1.0 - - - +
148A LYS 3.9 1.6 - - - -
149A PRO* 3.5 20.0 - - - +
173A BFS 3.1 21.2 + - - -
24B TYR* 5.1 0.6 + - - -
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Residues in contact with LEU 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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101A ILE* 3.3 35.7 - - + -
102A GLY 3.6 2.7 - - - -
103A TYR* 3.8 32.1 - - + +
130A ALA 3.9 1.4 + - - +
131A ASN* 1.3 71.6 - - - +
133A HIS* 1.3 73.7 + - - +
134A TRP* 4.1 20.4 - - + +
147A LEU* 3.2 2.9 - - - -
148A LYS* 2.7 67.3 + - + +
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Residues in contact with HIS 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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23A VAL* 3.8 2.6 - - + +
26A TRP* 3.5 38.8 - + - -
101A ILE* 3.3 6.4 - - - -
102A GLY 2.9 30.2 + - - +
104A HIS* 3.3 19.0 - + + -
131A ASN* 3.3 30.8 + - + +
132A LEU* 1.3 86.4 - - - +
134A TRP* 1.3 60.9 + - - +
135A TYR* 2.9 36.8 + - + +
144A PHE* 3.3 16.6 - + + -
146A GLY 3.5 3.8 - - - +
147A LEU* 3.5 17.1 - - + +
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Residues in contact with TRP 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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47A ARG* 3.4 54.3 - - + -
49A ASP* 4.3 7.0 - - + -
100A VAL 3.8 1.8 - - - -
101A ILE* 3.8 31.1 - - + +
132A LEU* 4.1 18.7 - - + +
133A HIS* 1.3 75.3 - - - +
135A TYR* 1.3 59.3 + - - +
136A LYS* 6.0 0.4 - - + -
144A PHE* 3.8 2.6 - - - -
145A ALA* 2.8 42.5 + - + +
146A GLY 3.0 28.7 + - - +
147A LEU* 3.5 23.8 - - - -
148A LYS* 3.8 20.9 - - + -
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Residues in contact with TYR 135 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A LEU* 3.6 25.8 - - + -
22A CYS* 3.7 29.6 - - + -
23A VAL* 3.3 14.5 - - + +
92A TRP* 3.5 30.3 - + - -
99A GLU* 3.4 6.6 - - - +
100A VAL 2.8 41.9 + - - +
102A GLY 3.9 2.5 - - - -
104A HIS* 2.9 13.3 + - - -
133A HIS* 2.9 48.4 + - + -
134A TRP* 1.3 75.8 - - - +
136A LYS* 1.3 66.1 + - - +
142A TRP* 3.9 6.3 - - + -
143A LYS 3.1 14.8 - - - +
144A PHE* 4.0 11.9 - + - -
145A ALA 4.3 0.2 - - - +
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Residues in contact with LYS 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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43A ALA* 4.9 7.2 - - + -
45A THR 5.2 2.9 - - - +
98A ASP* 3.2 23.1 + - - +
99A GLU* 3.6 25.4 + - + +
134A TRP* 5.6 0.9 - - + -
135A TYR* 1.3 79.0 - - - +
137A LYS* 1.3 58.8 + - - +
138A ILE* 3.4 24.0 + - + -
142A TRP* 3.7 4.0 - - - -
143A LYS* 2.8 39.0 + - - +
145A ALA* 3.7 24.9 - - + -
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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