Contacts of the strand formed by residues 1 - 13 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 2.6 38.1 - - + +
1B MET* 4.2 11.7 - - - +
92B GLY* 5.0 5.2 - - - -
93B ASN* 4.2 0.9 - - - +
153B LEU* 3.1 26.3 - - + +
0C ALA* 1.3 81.5 - - - +
2C ARG* 1.3 68.7 + - - +
92C GLY* 4.9 1.1 - - - -
153C LEU* 3.0 48.2 - - + -
154C LEU 3.2 11.9 - - - +
155C MET* 3.6 41.7 - - + +
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Residues in contact with ARG 2 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B GLY 4.7 3.2 + - - -
93B ASN* 3.3 27.6 - - - +
94B VAL 5.7 0.2 + - - -
125B ASP* 2.6 36.3 + - - -
126B GLU* 3.9 20.6 - - - +
128B ASN* 5.9 0.6 - - - +
153B LEU* 4.0 1.1 - - - -
0C ALA* 4.6 4.9 - - - +
1C MET* 1.3 82.2 - - - +
3C ILE* 1.3 59.5 - - - +
50C GLY 4.9 0.6 + - - -
51C ALA* 3.0 31.7 + - + +
53C ALA* 3.5 16.0 - - - +
89C TYR* 3.7 38.2 + - + -
152C ALA 3.6 0.7 - - - +
153C LEU* 3.2 8.9 - - - +
154C LEU* 2.8 37.5 + - + +
156C LYS* 4.6 6.4 - - + +
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Residues in contact with ILE 3 (chain C).
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* 3.3 20.9 - - + -
3B ILE* 3.3 42.0 - - + -
93B ASN* 2.8 39.2 + - - +
95B ASP* 4.0 4.0 - - - +
151B VAL* 3.8 31.9 - - + +
152B ALA* 4.0 8.1 - - - +
153B LEU* 4.0 25.3 - - + +
2C ARG* 1.3 73.9 - - - +
4C GLY* 1.3 62.3 + - - +
51C ALA* 3.3 9.3 - - - -
152C ALA 3.2 4.0 - - - -
153C LEU* 4.7 5.6 - - + +
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Residues in contact with GLY 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ASP* 3.5 12.3 - - - -
151B VAL* 4.1 4.0 - - - -
3C ILE* 1.3 78.1 - - - +
5C HIS* 1.3 62.6 + - - +
47C ALA* 3.4 22.0 - - - -
51C ALA* 3.7 3.0 - - - +
151C VAL* 3.2 9.4 - - - +
152C ALA 2.9 31.6 + - - +
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Residues in contact with HIS 5 (chain C).
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* 5.1 6.1 - + - -
5B HIS* 5.2 2.0 - + - -
95B ASP* 3.1 8.4 + - - +
97B THR* 3.0 25.2 + - - +
130B LYS* 2.7 29.6 + - - +
149B GLU* 3.5 31.3 + - + +
150B ALA* 5.7 0.4 - - - -
151B VAL* 3.8 28.7 - - + +
4C GLY* 1.3 75.4 - - - +
6C GLY* 1.3 77.0 + - - +
7C PHE* 4.0 7.2 - - + -
47C ALA* 3.7 7.5 - - - +
149C GLU* 2.8 30.7 + - - -
150C ALA 3.3 13.7 - - - -
151C VAL* 4.2 11.4 - - + -
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Residues in contact with GLY 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B LYS* 4.5 2.5 - - - -
5C HIS* 1.3 81.9 - - - +
7C PHE* 1.3 62.4 + - - +
43C ALA* 3.4 22.4 - - - -
46C ASP* 3.9 7.4 - - - -
47C ALA* 3.7 5.0 - - - +
149C GLU* 3.2 4.0 - - - -
150C ALA 2.8 33.2 + - - +
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Residues in contact with PHE 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B THR* 4.2 13.5 - - + +
99B ILE* 4.1 17.7 - - + -
132B THR* 2.9 37.7 + - + -
133B THR 5.6 0.7 - - - -
134B THR* 4.1 17.3 - - + -
149B GLU* 4.2 5.4 - - - +
5C HIS* 4.0 11.7 - - + -
6C GLY* 1.3 74.4 - - - +
8C ASP* 1.3 62.4 + - - +
9C VAL* 3.8 28.7 - - + -
43C ALA* 3.9 4.8 - - - +
46C ASP* 4.3 9.6 + - - +
99C ILE* 4.7 5.8 - - + -
139C PHE* 5.3 3.8 - + - -
147C ALA* 4.2 17.5 - - + -
148C CYS 3.3 9.4 - - - -
149C GLU* 3.3 34.5 - - + -
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Residues in contact with ASP 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B THR* 4.0 7.1 + - - -
133B THR 4.6 0.5 - - - +
7C PHE* 1.3 77.6 - - - +
9C VAL* 1.3 79.5 + - - +
10C HIS* 3.4 12.6 + - - -
39C VAL* 3.6 22.3 - - - +
42C HIS* 2.7 40.8 + - + +
43C ALA* 4.0 2.4 - - - +
57C ILE* 5.3 1.5 - - + +
147C ALA* 3.3 1.2 - - - +
148C CYS 2.9 32.4 + - - +
305C MG 1.9 32.0 - - - -
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Residues in contact with VAL 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B THR 4.1 3.3 + - - +
134B THR* 3.6 36.6 - - + +
135B GLU* 3.4 13.8 - - + +
137B LEU* 4.1 4.3 - - + -
7C PHE* 3.8 20.2 - - + -
8C ASP* 1.3 88.7 + - - +
10C HIS* 1.3 86.7 + - - +
39C VAL* 4.0 1.1 - - - -
139C PHE* 3.8 34.5 - - + -
146C ILE 3.4 9.9 - - - +
147C ALA* 3.8 7.0 - - + -
305C MG 4.2 0.7 - - - -
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Residues in contact with HIS 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B GLU* 4.0 20.9 + - - +
8C ASP* 3.4 25.3 + - - -
9C VAL* 1.3 87.0 + - - +
11C ALA* 1.3 61.5 + - - +
31C LEU* 3.6 17.6 - - + +
32C LEU 3.2 20.6 + - - +
33C ALA* 3.4 21.2 - - + +
34C HIS 5.2 1.3 - - - -
35C SER* 5.1 0.4 - - - -
37C GLY* 3.5 23.8 - - - +
39C VAL* 3.5 13.5 - - + +
42C HIS* 3.4 17.7 + + - -
63C ASP* 5.7 2.2 - - - -
145C GLY* 3.2 2.4 - - - -
146C ILE* 3.0 30.6 + - - +
302C GOL 4.7 8.1 - - - -
305C MG 4.2 5.0 - - - -
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Residues in contact with ALA 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B GLU* 4.8 12.7 - - + +
137B LEU* 3.8 24.8 - - + +
10C HIS* 1.3 73.7 - - - +
12C PHE* 1.3 65.6 + - - +
31C LEU* 3.4 4.9 - - - +
32C LEU* 2.8 43.9 + - + +
144C GLU 3.4 9.0 - - - +
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Residues in contact with PHE 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ALA* 1.3 77.4 - - - +
13C GLY* 1.3 57.7 + - - +
18C ILE* 4.4 3.4 - - + -
27C TYR* 3.5 32.5 - + - -
29C LYS* 3.8 27.1 - - + -
30C GLY 3.1 14.6 - - - +
31C LEU* 3.4 14.6 - - + -
32C LEU* 3.7 10.2 - - - +
102C ALA 3.8 8.1 - - - -
143C GLY* 3.2 29.8 - - - +
144C GLU 3.0 12.1 + - - +
145C GLY* 3.6 24.8 - - - -
146C ILE* 3.2 37.7 - - + -
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Residues in contact with GLY 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ALA 3.9 0.6 + - - -
12C PHE* 1.3 76.1 - - - +
14C GLY* 1.3 68.1 + - - -
15C GLU 3.7 0.2 + - - -
29C LYS* 4.9 2.2 - - - -
30C GLY* 2.7 25.6 + - - +
31C LEU 4.9 0.7 - - - +
32C LEU* 4.0 24.5 - - - +
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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