Contacts of the strand formed by residues 114 - 125 (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 VAL 114 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15G HIS* 3.5 32.1 - - + +
16G ARG* 3.1 8.0 - - - +
17G ALA* 2.9 43.8 + - + +
105G PHE* 3.8 30.7 - - + +
107G HIS* 3.3 43.3 - - + +
113G PRO* 1.3 73.5 - - - +
115G ASN* 1.3 64.6 + - - +
116G HIS* 3.9 7.2 - - + +
204G SO4 4.6 3.8 - - - +
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Residues in contact with ASN 115 (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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16A ARG* 4.4 19.6 - - - +
113A PRO* 5.3 11.1 + - - +
114A VAL 5.3 0.8 + - - -
115A ASN* 3.0 47.3 + - - +
15G HIS 3.8 2.4 - - - +
16G ARG* 2.6 45.7 + - - +
35G PHE* 5.6 1.0 - - - -
113G PRO* 3.8 4.4 + - + +
114G VAL* 1.3 73.7 - - - +
116G HIS* 1.3 60.0 + - - +
117G LEU* 4.1 1.0 + - - +
204G SO4 4.2 15.0 + - - -
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Residues in contact with HIS 116 (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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37A ARG* 4.0 14.8 + - - -
115A ASN* 4.6 0.2 + - - -
14G GLY* 3.2 15.4 - - - -
15G HIS* 3.1 31.4 + - + +
35G PHE* 4.7 0.3 - - - -
102G TYR* 3.6 19.5 - + - -
103G ASP 5.6 0.2 - - - -
105G PHE* 4.0 20.2 - + + -
114G VAL* 4.0 5.2 - - + -
115G ASN* 1.3 74.9 - - - +
117G LEU* 1.3 98.0 + - - +
118G ARG* 4.3 10.5 - - + +
204G SO4 2.3 32.6 + - - +
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Residues in contact with LEU 117 (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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12A GLU* 5.2 0.2 - - - +
37A ARG* 3.0 28.7 + - - +
115A ASN* 3.2 49.1 - - - +
116A HIS 4.4 0.2 - - - -
117A LEU* 3.3 31.6 - - + +
12G GLU* 4.4 15.7 - - + +
13G LEU 3.5 2.2 - - - +
14G GLY* 4.1 3.1 - - - -
16G ARG* 6.2 0.2 - - - +
35G PHE* 3.6 30.7 - - + -
37G ARG* 4.2 12.8 - - - +
115G ASN* 4.1 0.8 + - - +
116G HIS* 1.3 94.3 + - - +
118G ARG* 1.3 63.2 + - - +
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Residues in contact with ARG 118 (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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12A GLU* 5.1 3.8 - - - +
40A GLU* 3.8 30.8 + - + +
117A LEU* 4.1 3.6 - - - -
12G GLU* 3.5 5.5 - - - +
13G LEU* 2.5 53.3 + - - +
100G PHE* 3.5 31.7 - - - +
101G ASP 3.5 25.3 + - - +
102G TYR* 3.9 30.1 - - + +
103G ASP 5.0 0.6 - - - +
116G HIS* 4.3 12.1 - - - +
117G LEU* 1.3 76.4 - - - +
119G CYS* 1.3 64.6 + - - +
120G GLU* 2.6 31.7 + - + +
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Residues in contact with CYS 119 (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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10A LYS* 6.4 2.2 - - - -
12A GLU* 3.5 16.1 + - - -
39A PRO* 6.0 0.9 - - - -
117A LEU* 4.0 7.1 - - + +
119A CYS* 2.0 46.2 - - + -
11G LEU 3.6 6.5 - - - +
12G GLU* 4.9 5.4 - - + +
118G ARG* 1.3 77.0 - - - +
120G GLU* 1.3 74.6 + - - +
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Residues in contact with GLU 120 (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* 4.3 5.0 - - - +
10G LYS* 3.7 2.1 - - - +
11G LEU* 2.8 48.5 + - + +
13G LEU* 4.4 11.0 - - + -
100G PHE* 3.6 43.0 - - + -
118G ARG* 2.6 38.4 + - + +
119G CYS* 1.3 82.2 - - - +
121G LYS* 1.3 65.0 + - - +
122G LEU* 4.0 1.5 + - + -
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Residues in contact with LYS 121 (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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121A LYS* 5.6 14.9 - - - +
8G GLN* 3.7 46.5 + - + +
9G VAL 3.7 6.5 - - - +
10G LYS* 4.4 34.9 - - + +
120G GLU* 1.3 76.7 + - - +
122G LEU* 1.3 73.4 + - - +
123G THR* 4.1 3.5 + - - +
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Residues in contact with LEU 122 (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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7G VAL 3.6 0.7 - - - +
8G GLN* 3.1 8.0 - - - +
9G VAL* 2.9 56.3 + - + +
11G LEU* 3.6 30.1 - - + -
47G PHE* 4.6 1.1 - - + -
89G PHE* 3.7 31.2 - - + -
98G VAL* 4.0 16.6 - - + -
100G PHE* 4.0 25.6 - - + -
120G GLU* 5.0 1.1 - - + +
121G LYS* 1.3 79.5 - - - +
123G THR* 1.3 60.4 + - - +
124G PHE* 4.1 8.7 - - + -
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Residues in contact with THR 123 (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 ALA* 4.6 11.7 - - + -
7G VAL 3.6 2.9 - - - +
8G GLN* 3.1 35.1 + - + +
121G LYS* 4.1 4.6 + - - +
122G LEU* 1.3 74.8 - - - +
124G PHE* 1.3 67.2 + - - +
125G ASN* 3.9 27.8 + - - +
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Residues in contact with PHE 124 (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 CYS 3.5 2.9 - - - +
6G ALA* 3.6 1.0 - - - -
7G VAL* 2.9 39.0 + - + +
9G VAL* 3.9 19.7 - - + -
89G PHE* 3.6 49.8 - + - -
91G ASN* 4.0 8.3 - - - -
95G PRO* 4.6 17.0 - - + -
122G LEU* 4.1 10.1 - - + -
123G THR* 1.3 77.3 - - - +
125G ASN* 1.3 64.1 + - - +
126G ASN 3.6 0.5 + - - -
127G PRO* 3.7 14.7 - - + +
131G PHE* 3.9 20.2 - + - -
135G LEU* 3.7 36.6 - - + -
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Residues in contact with ASN 125 (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 SER* 6.4 0.4 - - - -
5G CYS 3.6 3.5 - - - +
6G ALA* 4.4 9.9 - - - +
93G GLU* 5.4 0.7 - - - +
123G THR* 4.2 24.7 + - - +
124G PHE* 1.3 71.0 - - - +
126G ASN* 1.3 78.6 + - - +
127G PRO* 3.6 0.7 - - - +
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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