Contacts of the strand formed by residues 114 - 125 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A HIS* 3.3 31.2 - - + +
16A ARG* 3.2 9.0 - - - +
17A ALA* 2.8 49.0 + - + +
105A PHE* 3.5 24.5 - - + +
106A LEU 4.0 0.7 - - - -
107A HIS* 3.3 50.0 - - + +
113A PRO* 1.3 73.3 - - - +
115A ASN* 1.3 63.8 + - - +
116A HIS* 4.2 5.2 - - + +
115G ASN* 5.3 0.7 + - - -
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Residues in contact with ASN 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A HIS 3.8 2.6 - - - +
16A ARG* 3.3 18.2 - - + +
35A PHE* 5.8 2.9 - - - -
113A PRO 3.7 3.9 + - - +
114A VAL* 1.3 74.4 - - - +
116A HIS* 1.3 62.3 + - - +
16G ARG* 4.5 5.5 - - - +
37G ARG* 4.6 7.0 + - - +
115G ASN* 3.0 59.5 + - - +
116G HIS 4.5 0.6 - - - -
117G LEU* 3.2 39.6 - - + +
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Residues in contact with HIS 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLY* 3.2 4.0 - - - -
15A HIS* 3.1 51.2 + - + +
35A PHE* 4.9 2.3 - - - -
102A TYR* 3.5 15.7 + + - -
103A ASP 6.0 0.2 - - - -
105A PHE* 3.8 31.3 - + + -
114A VAL* 4.3 0.4 - - + -
115A ASN* 1.3 77.7 + - - +
117A LEU* 1.3 78.8 + - - +
118A ARG* 3.9 18.1 + - + -
12G GLU* 6.1 0.7 - - - -
40G GLU* 4.2 24.0 + - + +
117G LEU* 4.4 1.3 - - - -
203G SO4 5.1 4.2 + - - -
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Residues in contact with LEU 117 (chain A).
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* 4.2 20.9 - - + +
13A LEU 3.5 17.7 - - - +
35A PHE* 4.1 14.8 - - + -
37A ARG* 3.8 17.3 - - - +
116A HIS* 1.3 88.3 + - - +
118A ARG* 1.3 62.1 + - - +
119A CYS* 4.3 7.0 - - - -
12G GLU* 4.3 16.7 + - + +
39G PRO* 6.0 0.7 - - - +
117G LEU* 3.3 50.6 - - + +
118G ARG* 4.0 4.0 - - - +
119G CYS* 4.0 21.5 - - + +
203G SO4 5.1 5.7 + - - -
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Residues in contact with ARG 118 (chain A).
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* 3.7 0.7 - - - -
13A LEU* 2.6 51.6 + - + +
100A PHE* 3.8 21.8 - - - +
101A ASP 3.5 25.1 + - - -
102A TYR* 4.2 19.4 - - + +
103A ASP* 4.8 2.6 - - - +
116A HIS* 3.9 16.2 - - + +
117A LEU* 1.3 75.6 - - - +
119A CYS* 1.3 63.9 + - - +
120A GLU* 2.7 32.9 + - + +
202A SO4 2.8 33.3 + - - -
203G SO4 5.9 1.8 - - - +
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Residues in contact with CYS 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU 3.6 5.8 - - - +
12A GLU* 3.8 15.9 - - - -
117A LEU* 4.4 6.7 - - - -
118A ARG* 1.3 76.9 - - - +
120A GLU* 1.3 70.8 + - - +
121A LYS 4.4 0.3 + - - -
10G LYS* 5.2 12.0 + - - +
119G CYS* 2.0 53.8 - - + -
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Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A LYS* 3.8 2.3 - - - +
11A LEU* 2.8 46.1 + - + +
13A LEU* 3.7 19.1 - - + -
100A PHE* 3.6 35.5 - - + -
118A ARG* 2.7 37.2 + - - +
119A CYS* 1.3 83.1 - - - +
121A LYS* 1.3 66.4 + - - +
122A LEU* 3.8 1.6 + - + -
202A SO4 5.5 1.5 + - - -
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Residues in contact with LYS 121 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A GLN* 3.2 43.2 + - + +
9A VAL 3.9 6.7 - - - +
10A LYS* 5.1 12.6 - - + +
119A CYS 4.4 0.2 - - - -
120A GLU* 1.3 75.6 + - - +
122A LEU* 1.3 73.0 + - - +
123A THR* 4.1 4.6 + - - +
8G GLN* 5.5 6.1 - - - +
121G LYS* 5.6 13.4 - - - +
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL 3.6 1.2 - - - +
8A GLN* 3.2 7.1 - - - +
9A VAL* 3.0 54.3 + - + +
11A LEU* 3.6 34.5 - - + -
47A PHE* 5.0 0.4 - - + -
89A PHE* 3.8 29.8 - - + -
98A VAL* 4.0 15.5 - - + -
100A PHE* 4.0 24.2 - - + -
120A GLU* 4.7 3.8 - - + +
121A LYS* 1.3 80.6 - - - +
123A THR* 1.3 61.7 + - - +
124A PHE* 4.1 7.4 - - + -
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Residues in contact with THR 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ALA* 4.1 20.0 - - + -
7A VAL 3.6 2.5 - - - +
8A GLN* 3.6 24.1 + - + +
121A LYS* 4.1 6.7 + - - +
122A LEU* 1.3 74.1 - - - +
124A PHE* 1.3 65.2 + - - +
125A ASN* 3.9 28.8 + - - +
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Residues in contact with PHE 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A CYS 3.6 0.9 - - - +
6A ALA* 3.5 2.9 - - - -
7A VAL* 2.8 50.0 + - + +
9A VAL* 3.7 27.8 - - + -
89A PHE* 3.4 52.5 - + - -
95A PRO* 4.4 23.3 - - + -
122A LEU* 4.1 9.9 - - + -
123A THR* 1.3 74.2 - - - +
125A ASN* 1.3 62.4 + - - +
126A ASN 3.8 0.5 + - - -
127A PRO* 4.1 10.9 - - + +
131A PHE* 4.0 17.5 - + - -
135A LEU* 3.8 34.1 - - + -
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Residues in contact with ASN 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A CYS 3.6 4.1 - - - +
6A ALA* 4.2 9.5 - - - +
123A THR* 3.9 27.8 + - - +
124A PHE* 1.3 71.7 - - - +
126A ASN* 1.3 81.6 + - - +
127A PRO* 3.5 1.3 - - - +
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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