Contacts of the strand formed by residues 100 - 108 (chain G) in PDB entry 4GG6
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 ALA 100 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43G ARG* 4.6 4.7 - - + -
44G GLN 3.3 28.9 - - - +
45G LEU* 3.6 14.4 - - + +
46G PRO* 4.4 6.5 - - - -
98G ASP 3.3 5.3 + - - +
99G ALA* 1.3 75.0 - - - +
101G VAL* 1.3 64.5 + - - +
102G TYR* 3.4 18.3 - - + +
123G HIS* 4.8 2.0 - - - -
124G LEU 3.0 27.9 + - - -
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Residues in contact with VAL 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G TYR 3.7 0.3 - - - +
43G ARG* 3.0 6.9 - - - -
44G GLN* 2.8 42.6 + - + +
46G PRO* 6.0 2.7 - - + -
100G ALA* 1.3 76.2 - - - +
102G TYR* 1.3 63.2 + - - +
103G TYR* 3.8 31.5 + - + +
120G LYS 3.9 16.6 - - - +
121G GLY 4.1 0.2 - - - -
122G THR 3.2 17.0 - - - +
123G HIS* 3.5 35.7 - - + +
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Residues in contact with TYR 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G GLN* 2.8 21.7 + - - -
21G LEU* 3.7 16.6 - - + -
41G TRP* 4.2 8.7 - + + -
42G TYR 3.3 6.7 - - - -
43G ARG* 3.6 40.7 + - + -
53G VAL* 4.6 4.3 - - + -
89G LEU* 3.5 29.2 - - + -
91G LEU* 4.0 16.4 - - + +
98G ASP* 2.8 32.5 + - - +
100G ALA* 3.4 25.1 - - + +
101G VAL* 1.3 73.3 - - - +
103G TYR* 1.3 61.1 + - - +
122G THR* 2.7 32.6 + - - +
124G LEU* 3.7 21.8 - - + -
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Residues in contact with TYR 103 (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 GLN* 4.0 0.2 - - - -
40G HIS 3.6 0.9 - - - +
41G TRP* 3.3 10.5 - - - -
42G TYR* 2.8 43.7 + - + +
43G ARG 4.8 0.4 - - - -
44G GLN* 2.6 42.5 + - + -
50G PRO* 4.9 5.2 - - + -
101G VAL* 3.8 20.0 - - + +
102G TYR* 1.3 72.3 - - - +
104G CYS* 1.3 59.7 + - - +
105G ILE* 4.1 6.5 - - + +
118G PHE* 3.7 44.4 - + + -
119G GLY 3.9 13.0 - - - -
120G LYS 3.5 22.0 - - - -
121G GLY* 3.5 18.2 - - - -
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Residues in contact with CYS 104 (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 THR* 2.7 28.5 + - - -
6G GLN* 3.2 23.3 + - - +
23G CYS* 2.0 51.4 - - + -
25G HIS* 4.3 6.7 - - - -
39G ILE* 4.3 5.4 - - - -
40G HIS 3.4 3.4 - - - -
41G TRP* 3.7 19.7 - - + -
87G SER* 4.2 5.4 - - - -
103G TYR* 1.3 74.0 - - - +
105G ILE* 1.3 69.0 + - - +
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Residues in contact with ILE 105 (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 THR* 4.6 1.1 - - - -
38G TYR 3.6 0.5 - - - +
39G ILE* 3.5 5.2 - - - +
40G HIS* 2.7 52.5 + - + +
42G TYR* 5.4 0.4 - - + -
103G TYR* 4.2 6.7 - - + -
104G CYS* 1.3 88.8 - - - +
106G LEU* 1.3 71.8 + - - +
107G ARG* 3.8 13.0 - - + +
115G GLY* 3.3 27.4 - - - +
117G THR 4.1 6.3 - - - +
118G PHE* 3.6 51.4 - - + -
119G GLY 4.1 7.6 - - - +
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Residues in contact with LEU 106 (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 LYS 5.0 7.9 - - - +
4G THR* 3.9 16.8 - - + +
25G HIS* 3.8 30.3 - - + -
27G THR* 4.9 2.7 - - - +
28G ILE* 3.7 48.7 - - + +
37G ASP* 4.3 13.7 - - - +
38G TYR 3.4 3.8 - - - +
39G ILE* 3.8 17.9 - - + -
105G ILE* 1.3 81.2 - - - +
107G ARG* 1.3 64.7 + - - +
114G ASP 5.0 0.3 - - - +
115G GLY* 3.7 12.8 - - - -
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Residues in contact with ARG 107 (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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37G ASP* 3.3 5.8 - - - -
38G TYR* 2.5 39.9 + - - +
40G HIS* 3.7 38.4 + - + +
42G TYR* 4.1 19.3 + - - -
105G ILE* 3.8 10.2 + - + +
106G LEU* 1.3 74.3 - - - +
108G ASP* 1.3 64.3 + - - +
111G GLY* 5.8 3.4 - - - -
114G ASP 5.6 0.2 - - - -
115G GLY* 2.8 29.7 + - - +
116G LEU* 3.1 44.9 + - - +
118G PHE* 3.5 25.4 - - - -
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Residues in contact with ASP 108 (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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58A PHE* 3.9 12.1 - - + -
29G SER* 5.0 0.7 + - - -
36G THR* 3.4 23.0 - - - +
37G ASP* 3.5 11.2 + - - +
107G ARG* 1.3 77.1 - - - +
109G GLY* 1.3 59.2 + - - +
110G ARG* 2.9 58.8 + - - +
111G GLY* 2.7 43.2 + - - +
114G ASP 5.5 3.2 + - - -
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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