Contacts of the strand formed by residues 1 - 13 (chain A) in PDB entry 3GHZ
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 MET 1 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0A ALA* 1.3 74.9 - - - +
2A ARG* 1.3 71.7 + - - +
153A LEU* 4.0 19.5 - - + -
154A LEU 3.3 6.7 - - - +
155A MET* 4.3 16.4 - - + +
1B MET* 3.7 35.4 - - - +
153B LEU* 5.2 3.1 - - - -
1C MET* 2.6 54.5 - - + +
92C GLY* 5.3 3.1 - - - -
93C ASN* 4.3 0.2 - - - +
153C LEU* 3.4 18.4 - - + +
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Residues in contact with ARG 2 (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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0A ALA* 5.0 4.3 - - + +
1A MET* 1.3 83.1 - - - +
3A ILE* 1.3 60.0 + - - +
50A GLY 4.7 0.6 + - - -
51A ALA* 2.9 28.2 + - + +
52A ALA 4.2 0.6 + - - -
53A ALA* 3.4 20.8 - - - +
87A LYS* 5.3 0.8 - - - +
89A TYR* 3.7 38.2 + - + -
152A ALA 3.8 0.7 - - - +
153A LEU* 3.2 9.4 - - - +
154A LEU* 2.9 33.6 + - + +
156A LYS* 5.9 0.7 - - + -
92C GLY 4.9 2.7 - - - -
93C ASN* 3.3 30.8 - - - +
94C VAL 5.6 0.2 + - - -
125C ASP* 2.7 32.3 + - - +
126C GLU* 3.3 26.7 + - - +
127C VAL 5.6 0.4 - - - -
128C ASN* 5.8 0.2 - - - +
153C LEU* 4.5 0.4 - - - -
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Residues in contact with ILE 3 (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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2A ARG* 1.3 74.3 - - - +
4A GLY* 1.3 62.8 + - - +
51A ALA* 3.2 10.2 + - - -
152A ALA 3.5 3.1 - - - -
153A LEU* 4.6 5.2 - - + -
3B ILE* 3.2 27.6 - - + -
3C ILE* 3.3 34.5 - - + -
93C ASN* 2.8 48.0 + - - +
95C ASP* 4.0 4.7 - - - +
151C VAL* 3.6 33.4 - - + +
152C ALA* 4.1 3.8 - - - +
153C LEU* 3.8 27.3 - - + +
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Residues in contact with GLY 4 (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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3A ILE* 1.3 76.9 - - - +
5A HIS* 1.3 60.1 + - - -
47A ALA* 3.2 24.5 - - - -
51A ALA* 3.6 3.5 - - - +
151A VAL* 3.2 9.5 - - - +
152A ALA 3.0 29.6 + - - +
95C ASP* 3.4 11.2 - - - -
151C VAL* 4.0 3.4 - - - -
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Residues in contact with HIS 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLY* 1.3 73.4 - - - -
6A GLY* 1.3 74.2 + - - +
7A PHE* 4.0 6.3 - - + -
47A ALA* 3.6 6.6 - - - +
149A GLU* 2.8 24.9 + - + -
150A ALA 3.3 18.2 - - - -
151A VAL* 4.2 11.4 - - + -
5B HIS* 5.2 2.9 - + - -
5C HIS* 5.1 5.4 - + - -
95C ASP* 2.9 8.6 + - - +
97C THR* 2.9 26.1 + - - +
130C LYS* 2.8 30.0 + - - -
149C GLU* 3.1 35.9 + - + +
150C ALA* 5.6 0.4 - - - -
151C VAL* 3.8 31.6 - - + +
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Residues in contact with GLY 6 (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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5A HIS* 1.3 84.2 - - - +
7A PHE* 1.3 62.9 + - - +
43A ALA* 3.3 24.9 - - - -
46A ASP* 3.9 6.7 - - - -
47A ALA* 3.6 5.6 - - - +
149A GLU* 3.2 3.8 - - - -
150A ALA 2.9 30.5 + - - -
97C THR* 4.8 0.2 - - - -
130C LYS* 4.6 1.8 - - - -
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Residues in contact with PHE 7 (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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5A HIS* 4.0 11.9 - - + -
6A GLY* 1.3 74.5 - - - +
8A ASP* 1.4 62.3 + - - +
9A VAL* 3.7 28.3 - - + -
43A ALA* 4.0 4.0 - - - +
46A ASP* 4.3 9.8 + - - +
99A ILE* 4.8 4.9 - - + -
139A PHE* 5.3 3.6 - + - -
147A ALA* 4.1 18.4 - - + -
148A CYS 3.3 12.3 - - - -
149A GLU* 3.7 29.4 - - + -
97C THR* 4.0 14.1 - - + +
99C ILE* 3.8 34.1 - - + -
132C THR* 2.9 32.0 + - + -
133C THR 5.9 0.4 - - - -
134C THR* 4.2 4.9 - - + -
149C GLU* 4.3 4.0 - - - +
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Residues in contact with ASP 8 (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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7A PHE* 1.4 76.5 - - - +
9A VAL* 1.3 77.9 + - - +
10A HIS* 3.3 13.5 - - - -
39A VAL* 3.2 22.3 - - + +
42A HIS* 2.7 41.2 + - + +
43A ALA 4.0 3.4 - - - +
46A ASP* 6.1 0.4 - - - +
57A ILE* 5.3 2.0 - - + -
147A ALA* 3.2 4.3 - - - +
148A CYS 2.9 31.9 + - - +
304A MG 2.0 31.4 - - - -
132C THR* 3.9 6.0 + - - -
133C THR 4.5 0.3 - - - +
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Residues in contact with VAL 9 (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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7A PHE* 3.7 22.2 - - + -
8A ASP* 1.3 86.9 + - - +
10A HIS* 1.3 84.3 + - - +
39A VAL* 3.8 0.7 - - - -
139A PHE* 3.6 32.3 - - + -
146A ILE 3.4 8.3 - - - +
147A ALA* 3.8 11.7 - - + -
133C THR 4.2 2.8 + - - +
134C THR* 3.7 36.3 - - + +
135C GLU* 3.4 16.2 - - + +
137C LEU* 3.9 4.7 - - + -
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Residues in contact with HIS 10 (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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8A ASP* 3.3 28.4 + - - -
9A VAL* 1.3 84.0 + - - +
11A ALA* 1.3 60.3 + - - +
31A LEU* 3.7 13.9 - - + +
32A LEU 3.0 21.4 + - - +
33A ALA* 3.3 22.2 - - + +
34A HIS 5.0 1.3 - - - -
35A SER* 5.2 0.2 - - - -
37A GLY 3.6 20.9 - - - +
39A VAL* 3.8 13.6 - - + +
42A HIS* 3.4 17.3 + + - -
63A ASP* 5.6 1.3 - - - -
145A GLY* 3.1 3.3 - - - -
146A ILE 3.0 30.8 + - - -
303A GOL 5.0 6.9 + - - -
304A MG 4.2 3.2 - - - -
135C GLU* 3.8 25.2 + - - +
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Residues in contact with ALA 11 (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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9A VAL* 4.7 0.4 - - - +
10A HIS* 1.3 75.0 - - - +
12A PHE* 1.3 66.2 + - - +
31A LEU* 3.4 4.3 - - - -
32A LEU* 2.8 40.3 + - + -
144A GLU 3.5 8.5 - - - +
135C GLU* 4.7 13.6 - - + +
137C LEU* 3.7 25.3 - - + +
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Residues in contact with PHE 12 (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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11A ALA* 1.3 77.0 - - - +
13A GLY* 1.3 58.4 + - - +
18A ILE* 4.2 6.5 - - + -
27A TYR* 3.7 37.9 - + - -
29A LYS* 3.9 22.9 - - + -
30A GLY 3.3 15.5 - - - +
31A LEU* 3.5 17.3 - - + -
32A LEU* 4.0 9.1 - - - +
102A ALA 3.8 9.6 - - - -
143A GLY* 3.1 30.3 - - - +
144A GLU* 2.9 12.6 + - - +
145A GLY* 3.5 28.0 - - - -
146A ILE* 3.4 27.8 - - + -
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Residues in contact with GLY 13 (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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11A ALA 3.8 1.4 + - - -
12A PHE* 1.3 75.1 - - - +
14A GLY* 1.3 67.4 + - - -
29A LYS* 4.5 4.0 - - - +
30A GLY* 2.9 24.8 + - - +
31A LEU 3.8 1.7 + - - +
32A LEU* 3.7 25.0 - - - +
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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