Contacts of the strand formed by residues 97 - 104 (chain G) in PDB entry 5HJD
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 LYS 97 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86G GLU* 3.4 27.3 + - - +
87G VAL 3.3 15.0 - - - +
88G TYR* 3.5 39.5 + - + -
89G PHE* 3.8 6.5 - - - -
94G GLU* 5.1 0.4 + - - -
95G PRO* 3.2 17.6 - - - +
96G ARG* 1.3 84.3 - - + +
98G VAL* 1.3 67.6 + - - +
99G ARG* 6.0 2.0 - - - -
202G SO4 3.4 24.2 + - - +
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Residues in contact with VAL 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G LEU* 5.1 0.2 - - + -
85G ILE 3.8 0.7 - - - +
86G GLU* 3.4 3.0 - - - +
87G VAL* 2.9 38.8 + - + +
89G PHE* 3.5 26.0 - - + -
95G PRO* 6.5 0.2 - - + -
97G LYS* 1.3 80.8 - - - +
99G ARG* 1.3 65.5 + - - +
100G PHE* 3.7 37.6 - - + -
122G LEU* 4.0 17.5 - - + -
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Residues in contact with ARG 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G PRO* 3.9 23.0 - - + +
85G ILE 3.3 10.8 - - - +
86G GLU* 4.1 22.9 - - + +
97G LYS* 6.0 2.9 - - + -
98G VAL* 1.3 79.9 - - - +
100G PHE* 1.3 75.6 + - - +
101G ASP* 3.1 30.8 + - - -
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Residues in contact with PHE 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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11G LEU* 4.4 13.7 - - + -
13G LEU* 3.7 30.1 - - + -
84G PRO* 3.4 2.1 - - - +
85G ILE* 2.7 46.8 + - + +
87G VAL* 4.5 9.0 - - + -
98G VAL* 3.7 41.5 - - + -
99G ARG* 1.3 78.9 - - - +
101G ASP* 1.3 63.8 + - - +
102G TYR 3.4 2.5 + - - +
118G ARG* 3.5 25.4 - - - +
120G GLU* 3.6 35.7 - - + -
122G LEU* 4.0 11.9 - - + -
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Residues in contact with ASP 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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40A GLU* 5.0 4.5 - - - +
82G ILE* 4.0 23.1 - - + +
83G LEU 4.4 1.8 - - - -
84G PRO* 4.0 6.1 - - - +
99G ARG* 3.1 40.6 + - - -
100G PHE* 1.3 69.5 - - - +
102G TYR* 1.3 62.2 + - - +
103G ASP 3.7 2.1 + - - -
118G ARG* 3.5 14.4 + - - +
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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
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13G LEU* 3.9 33.9 - - + -
14G GLY* 3.1 9.6 - - - -
15G HIS* 2.5 57.2 + + + -
34G VAL* 4.0 14.1 - - + -
82G ILE* 3.5 2.0 - - - -
83G LEU* 2.6 51.8 + - + +
85G ILE* 3.8 16.8 - - + -
100G PHE 3.4 1.4 + - - +
101G ASP* 1.3 72.6 - - - +
103G ASP* 1.3 73.9 + - - +
104G LEU* 3.2 12.0 + - + -
116G HIS* 3.6 13.1 - + - -
118G ARG* 3.9 26.9 - - + +
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Residues in contact with ASP 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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41A HIS* 5.1 13.7 - - + -
15G HIS* 3.8 0.2 - - - -
81G PHE 4.0 0.2 - - - +
82G ILE* 3.9 19.1 - - + -
101G ASP 3.7 3.6 + - - +
102G TYR* 1.3 85.0 - - - +
104G LEU* 1.3 58.2 + - - +
105G PHE* 3.1 37.7 + - + +
116G HIS* 5.6 0.2 - - - -
118G ARG* 5.0 0.8 - - - +
17L ARG* 3.1 31.0 + - - -
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Residues in contact with LEU 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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15G HIS* 3.8 20.6 - - + -
32G TRP* 3.6 60.3 - - + +
34G VAL* 3.8 24.5 - - + -
79G ALA 4.9 0.2 - - - +
80G GLY* 3.1 8.1 - - - -
81G PHE* 3.0 51.0 + - + +
83G LEU* 3.9 17.5 - - + -
102G TYR* 3.2 10.0 + - + -
103G ASP* 1.3 69.2 - - - +
105G PHE* 1.3 59.0 + - - +
106G LEU* 4.2 7.9 - - + -
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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