Contacts of the strand formed by residues 89 - 102 (chain G) in PDB entry 3S4S
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 GLN 89 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1G LYS* 3.7 15.6 + - - +
17G THR 3.5 19.5 + - - +
18G ALA* 4.7 0.8 - - - +
19G SER* 5.4 1.2 + - - -
85G GLU* 3.4 7.6 - - - +
86G VAL* 2.7 42.5 + - + +
87G GLU* 4.1 15.4 + - - +
88G ASP* 1.3 74.5 - - - +
90G LYS* 1.3 69.4 + - - +
91G GLU* 3.4 30.1 + - + +
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Residues in contact with LYS 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1G LYS* 5.5 2.3 - - - +
33G GLN* 5.0 8.3 + - - +
83G ILE* 3.9 19.2 - - + +
84G CYS 3.6 3.1 - - - -
85G GLU* 2.5 42.7 + - + +
89G GLN* 1.3 82.5 - - - +
91G GLU* 1.3 64.5 + - - +
92G GLU* 3.5 6.3 + - + +
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Residues in contact with GLU 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1G LYS* 4.3 23.0 + - + +
15G THR* 3.7 9.8 + - - +
16G CYS* 3.4 19.2 - - - -
17G THR* 2.8 48.2 + - - +
28G TRP* 6.0 0.4 - - + -
82G TYR 3.8 0.7 - - - +
83G ILE* 3.4 4.7 - - - -
84G CYS* 3.0 40.3 + - + +
86G VAL* 3.8 4.6 - - + +
89G GLN* 3.4 24.6 - - - +
90G LYS* 1.3 71.5 - - - +
92G GLU* 1.3 61.1 + - - +
93G VAL* 5.1 2.4 - - + +
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Residues in contact with GLU 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G LYS* 3.2 26.8 + - + +
2G LYS* 3.1 22.3 + - - +
81G THR* 3.7 20.6 - - + +
82G TYR 3.6 1.1 - - - -
83G ILE* 3.7 29.0 - - + +
90G LYS* 3.5 5.8 + - + +
91G GLU* 1.3 75.8 - - - +
93G VAL* 1.3 63.4 + - - +
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Residues in contact with VAL 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G LYS* 3.3 20.4 - - + +
4G VAL* 3.8 28.3 - - + -
14G LEU* 3.9 20.9 - - + -
15G THR 5.1 4.7 - - - +
28G TRP* 3.5 29.6 - - + -
81G THR* 3.6 2.6 - - - +
82G TYR* 2.8 47.0 + - + +
91G GLU* 5.1 1.8 - - + +
92G GLU* 1.3 77.3 - - - +
94G GLN* 1.3 65.7 + - - +
95G LEU 3.8 1.0 + - - -
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Residues in contact with GLN 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G LYS 2.9 12.6 + - - +
3G VAL* 3.5 18.1 - - + +
4G VAL 2.9 28.2 + - - +
80G ASP* 3.5 12.6 - - - +
81G THR* 3.9 21.2 + - + +
93G VAL* 1.3 73.8 - - - +
95G LEU* 1.3 63.7 + - - +
96G LEU* 3.3 30.9 - - + +
122G PRO 5.7 2.0 + - - -
164G ASN* 5.0 5.9 + - - +
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Residues in contact with LEU 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G VAL* 3.4 19.3 - - + +
5G LEU 4.3 1.1 - - - -
6G GLY* 4.1 12.3 - - - +
12G VAL* 4.0 24.0 - - + -
14G LEU* 4.7 9.9 - - + -
71G ILE* 4.4 13.5 - - + -
74G LEU* 3.8 25.4 - - + -
78G ASP 4.0 15.3 - - - +
79G SER* 3.1 22.9 - - - -
80G ASP 2.7 19.1 + - - +
82G TYR* 4.1 11.9 - - + -
93G VAL 3.8 0.8 + - - -
94G GLN* 1.3 73.4 - - - +
96G LEU* 1.3 67.7 + - - +
97G VAL* 3.8 18.4 - - + -
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Residues in contact with LEU 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G VAL* 4.0 18.2 - - + -
4G VAL 3.0 6.5 + - - -
5G LEU* 3.3 22.1 - - + +
6G GLY 2.9 23.3 + - - +
79G SER* 3.5 2.2 - - - -
94G GLN* 3.3 42.8 - - + +
95G LEU* 1.3 76.5 - - - +
97G VAL* 1.3 62.8 + - - +
98G PHE* 4.0 10.5 - - + -
121G PRO* 3.5 22.7 - - + -
122G PRO 4.4 11.9 - - - +
123G GLY 5.4 1.1 - - - -
124G SER* 4.6 7.4 - - - -
163G GLN* 4.5 14.6 - - + +
164G ASN* 4.8 4.3 - - - +
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Residues in contact with VAL 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G GLY 3.3 4.9 - - - +
7G LYS 4.1 2.2 - - - -
8G LYS* 3.8 20.4 - - - +
74G LEU* 3.8 26.0 - - + -
75G LYS 3.5 25.4 - - - +
76G ILE* 3.5 24.5 - - + +
79G SER* 2.7 20.3 + - - +
95G LEU* 3.8 24.9 - - + -
96G LEU* 1.3 75.6 - - - +
98G PHE* 1.3 65.2 + - - +
121G PRO* 3.2 20.5 - - - +
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Residues in contact with PHE 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G LEU* 3.6 28.3 - - + -
6G GLY 2.9 12.7 + - - +
7G LYS* 3.5 0.3 - - - -
8G LYS 2.9 22.9 + - - -
76G ILE* 3.7 4.7 - - - -
96G LEU* 4.0 15.3 - - + -
97G VAL* 1.3 75.2 - - - +
99G GLY* 1.3 59.3 + - - +
118G LEU* 4.4 12.6 - - + -
119G GLU 3.3 6.5 - - - +
120G SER* 3.4 24.7 - - - -
121G PRO* 3.5 19.5 - - + -
124G SER* 3.9 9.9 - - - -
126G PRO* 4.1 10.3 - - + -
161G VAL* 4.4 12.3 - - + -
163G GLN* 3.7 30.1 - - + -
168G VAL* 4.4 8.3 - - + -
170G PHE* 3.3 23.7 - - + -
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Residues in contact with GLY 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G LYS* 4.1 16.8 - - - -
76G ILE* 3.7 2.8 - - - +
98G PHE* 1.3 74.3 - - - +
100G LEU* 1.3 60.1 + - - -
101G THR* 4.4 0.7 - - - -
118G LEU* 3.0 9.6 - - - +
119G GLU* 2.7 49.2 + - - -
170G PHE* 4.2 4.5 - - - -
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Residues in contact with LEU 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G GLY* 1.3 73.5 - - - +
101G THR* 1.3 75.3 + - - +
116G LEU* 4.5 16.2 - - + +
117G THR 3.6 22.9 - - - +
118G LEU* 3.7 20.6 - - + +
128G VAL* 5.1 6.7 - - + -
159G CYS* 3.5 29.2 - - + -
161G VAL* 5.1 2.5 - - + -
170G PHE* 3.4 51.4 - - + -
172G ILE* 4.8 14.6 - - + +
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Residues in contact with THR 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G LYS* 6.3 0.7 - - - +
100G LEU* 1.3 82.2 - - - +
102G ALA* 1.3 67.4 + - - +
116G LEU* 3.4 8.6 - - - +
117G THR* 3.0 38.6 + - - -
119G GLU* 5.7 4.5 - - - +
172G ILE* 4.3 8.1 - - - -
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Residues in contact with ALA 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101G THR* 1.3 80.0 + - - +
103G ASN* 1.3 65.9 + - - +
104G SER* 3.5 8.9 - - - +
114G LEU* 3.6 11.7 - - + -
115G THR 3.4 7.2 - - - -
116G LEU* 3.3 24.0 - - + -
117G THR* 5.6 0.4 - - - -
172G ILE* 3.7 17.4 - - + +
174G ILE* 5.4 4.5 - - + -
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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