Contacts of the strand formed by residues 3 - 19 (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 SER 3 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7E VAL* 5.2 0.9 - - - -
8E GLN 3.2 10.8 - - - -
9E VAL* 3.6 9.6 - - - +
135E LEU 2.9 28.3 + - - -
136E LEU* 4.0 16.7 - - - +
138E ALA* 3.8 17.0 + - - +
1G MET* 3.4 27.8 - - - +
2G ALA* 1.3 78.4 + - - +
4G SER* 1.3 67.4 + - - +
126G ASN* 3.9 3.1 - - - +
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Residues in contact with SER 4 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E ALA 3.2 7.6 - - - +
7E VAL* 3.3 3.4 - - - +
8E GLN* 3.2 44.8 + - - +
136E LEU* 4.1 5.0 - - - +
1G MET* 5.2 2.7 - - - -
3G SER* 1.3 79.5 + - - +
5G CYS* 1.3 62.4 + - - +
6G ALA* 3.9 1.9 + - - +
125G ASN* 6.4 0.7 - - - -
126G ASN* 3.1 20.0 - - - -
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Residues in contact with CYS 5 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E CYS* 2.0 48.0 - - - -
6E ALA 4.0 2.2 - - - -
7E VAL* 4.2 5.4 - - + -
132E ARG* 3.3 34.8 - - - +
136E LEU* 4.2 3.8 - - + +
4G SER* 1.3 75.0 - - - +
6G ALA* 1.3 59.8 + - - +
7G VAL* 3.6 16.4 - - - -
124G PHE 3.5 0.7 - - - +
125G ASN* 3.5 2.4 - - - +
126G ASN* 2.6 40.4 + - - +
127G PRO* 4.2 4.3 - - + -
132G ARG* 4.4 0.2 - - - -
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Residues in contact with ALA 6 (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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4E SER 3.3 10.1 - - - +
6E ALA* 3.4 31.3 + - + +
4G SER* 5.2 1.6 - - - +
5G CYS* 1.3 74.9 - - - +
7G VAL* 1.3 64.0 + - - +
8G GLN* 3.6 7.8 + - + +
123G THR* 4.6 9.9 - - + -
124G PHE 3.6 5.6 - - - -
125G ASN* 4.4 13.0 - - - +
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Residues in contact with VAL 7 (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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4E SER 3.2 9.6 - - - +
5E CYS* 4.0 9.4 - - + -
5G CYS* 3.6 24.9 - - - -
6G ALA* 1.3 71.6 - - - +
8G GLN* 1.3 63.3 + - - +
9G VAL* 4.5 6.5 - - + -
122G LEU 3.6 0.9 - - - +
123G THR* 3.6 1.4 - - - -
124G PHE* 2.9 40.7 + - - +
127G PRO* 3.9 17.5 - - + -
132G ARG* 4.2 11.2 - - + -
135G LEU* 3.7 37.5 - - + -
136G LEU* 4.2 13.7 - - + -
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Residues in contact with GLN 8 (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* 5.5 5.1 - - - +
2E ALA 4.6 0.3 - - - +
3E SER* 3.4 7.4 - - - -
4E SER* 3.0 39.7 + - - +
6G ALA* 4.3 7.9 - - + +
7G VAL* 1.3 76.3 - - - +
9G VAL* 1.3 62.8 + - - +
10G LYS* 5.7 1.1 - - - +
121G LYS* 3.7 40.6 + - + +
122G LEU 3.1 5.6 - - - +
123G THR* 3.1 35.2 + - + +
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Residues in contact with VAL 9 (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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2E ALA 4.8 0.4 - - - -
3E SER* 3.6 20.9 - - - +
7G VAL* 4.5 2.9 - - + -
8G GLN* 1.3 77.7 - - - +
10G LYS* 1.3 63.4 + - - +
47G PHE* 3.8 35.7 - - + -
121G LYS* 3.7 3.9 - - - +
122G LEU* 2.9 52.4 + - + +
124G PHE* 3.9 9.2 - - + -
135G LEU* 3.7 35.7 - - + +
138G ALA* 5.7 0.2 - - + -
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Residues in contact with LYS 10 (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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119A CYS* 5.2 12.9 + - - +
2E ALA* 4.1 26.0 + - + +
3E SER* 5.1 0.2 + - - -
8G GLN 5.7 0.9 - - - +
9G VAL* 1.3 77.9 - - - +
11G LEU* 1.3 70.9 + - - +
38G GLY* 4.1 2.9 - - - -
39G PRO* 3.4 27.6 - - + +
42G SER* 5.2 0.7 + - - -
44G ILE* 4.4 3.6 - - - +
47G PHE* 5.6 0.2 - - - -
120G GLU 3.8 4.9 - - - +
121G LYS* 4.4 32.2 - - + +
203G SO4 3.3 40.5 + - - +
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Residues in contact with LEU 11 (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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9G VAL* 5.5 0.2 - - + -
10G LYS* 1.3 82.8 - - - +
12G GLU* 1.3 61.6 + - - +
13G LEU* 4.2 10.5 - - + -
36G VAL* 4.5 8.1 - - + -
37G ARG 3.7 7.2 - - - +
39G PRO* 4.4 5.3 - - - +
44G ILE* 3.8 32.1 - - + -
47G PHE* 4.3 9.6 - - + -
48G VAL* 5.2 1.3 - - + -
87G VAL* 4.5 20.6 - - + -
100G PHE* 4.4 19.3 - - + -
119G CYS* 3.6 5.2 - - - +
120G GLU* 2.8 42.5 + - + +
122G LEU* 3.6 31.9 - - + -
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Residues in contact with GLU 12 (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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116A HIS* 6.1 0.9 - - - -
117A LEU* 4.3 18.6 + - + +
11G LEU* 1.3 75.4 - - - +
13G LEU* 1.3 62.5 + - - +
14G GLY 4.3 0.3 + - - -
35G PHE* 4.0 3.8 - - + +
36G VAL* 3.3 5.7 - - - -
37G ARG* 2.6 90.6 + - + +
39G PRO* 4.0 30.1 - - + +
40G GLU 5.1 1.1 + - - -
117G LEU* 4.4 21.1 - - + +
118G ARG 3.5 9.4 - - - +
119G CYS* 5.1 4.7 - - + -
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Residues in contact with LEU 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G LEU* 4.3 15.3 - - + -
12G GLU* 1.3 80.2 - - - +
14G GLY* 1.3 55.1 + - - +
35G PHE* 3.7 5.6 - - - +
36G VAL* 3.8 28.9 - - + -
85G ILE* 4.3 11.0 - - + -
100G PHE* 3.7 44.6 - - + -
102G TYR* 3.9 19.0 - - + -
117G LEU* 3.7 1.6 - - - -
118G ARG* 2.5 67.4 + - + +
120G GLU* 4.4 10.3 - - + -
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Residues in contact with GLY 14 (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* 1.3 75.8 - - - +
15G HIS* 1.3 63.1 + - - +
34G VAL* 3.5 2.4 - - - +
35G PHE* 2.9 51.6 + - - +
102G TYR* 3.1 14.1 + - - -
116G HIS 3.2 12.3 - - - -
117G LEU* 4.1 0.7 - - - -
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Residues in contact with HIS 15 (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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14G GLY* 1.3 74.7 - - - +
16G ARG* 1.3 71.4 + - - +
17G ALA* 4.3 6.7 - - + -
32G TRP* 5.0 0.4 - - + -
33G MET 3.1 13.9 - - - +
34G VAL* 3.8 11.0 - - + -
35G PHE* 3.7 5.0 - - - -
102G TYR* 2.5 38.6 + + + +
103G ASP 3.8 5.8 - - - -
104G LEU* 3.8 20.2 - - + -
105G PHE* 3.1 57.9 + + - -
114G VAL* 3.5 15.8 - - + +
115G ASN* 3.8 0.4 - - - -
116G HIS* 3.1 31.4 + - + +
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Residues in contact with ARG 16 (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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113A PRO* 6.0 2.2 - - - +
115A ASN* 4.5 6.9 - - - +
15G HIS* 1.3 73.7 - - - +
17G ALA* 1.3 60.0 + - - +
18G GLN* 4.2 1.3 - - + -
31G ASP 4.7 0.4 - - - -
32G TRP* 3.0 7.6 - - - +
33G MET* 2.9 59.8 + - + +
35G PHE* 4.2 10.8 - - - -
37G ARG* 4.6 7.7 - - - +
114G VAL 3.1 5.8 - - - +
115G ASN* 2.6 63.0 + - - +
117G LEU* 6.2 0.6 - - - +
201G SO4 3.6 23.0 + - - -
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Residues in contact with ALA 17 (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* 4.3 3.4 - - + -
16G ARG* 1.3 75.9 - - - +
18G GLN* 1.3 61.0 + - - +
19G VAL* 4.3 1.0 + - - +
30G HIS* 5.1 3.9 - - + -
31G ASP 3.7 4.9 - - - -
32G TRP* 3.9 2.9 - - + -
105G PHE 4.1 3.1 - - - +
106G LEU* 3.6 32.8 - - + -
107G HIS* 5.2 2.5 + - - +
113G PRO* 3.5 6.3 - - - +
114G VAL* 2.9 51.3 + - + +
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Residues in contact with GLN 18 (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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16G ARG* 4.2 1.3 - - + -
17G ALA* 1.3 75.9 - - - +
19G VAL* 1.3 72.7 + - - +
30G HIS* 3.4 7.8 - - - +
31G ASP* 2.7 44.2 + - + +
113G PRO* 4.4 17.2 - - + +
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Residues in contact with VAL 19 (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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17G ALA 4.3 1.3 + - - +
18G GLN* 1.3 86.8 + - - +
20G ARG* 1.3 74.9 + - - +
21G LYS* 3.7 1.9 + - - +
29G THR* 4.1 11.0 - - - +
30G HIS* 3.5 28.7 - - + +
107G HIS* 4.2 1.8 - - + +
108G LEU 4.1 18.8 - - - +
109G GLU* 4.1 33.9 - - + +
111G HIS 5.4 3.1 - - - +
113G PRO* 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