Contacts of the strand formed by residues 5 - 14 (chain A) in PDB entry 5IZL
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 ARG 5 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ALA* 3.6 22.8 - - - +
3A GLY 3.9 11.4 + - - +
4A ARG* 1.3 77.3 - - - +
6A VAL* 1.3 69.1 + - - +
7A ASN 4.3 0.2 - - - -
57A SER* 4.1 17.4 - - - -
68A LEU* 5.2 3.1 - - - -
69A PRO* 4.6 11.4 - - - +
85A LEU* 3.3 34.8 - - + +
87A GLN* 3.3 34.0 - - - +
273A PHE* 3.8 60.2 + - + +
274A HIS* 5.5 5.8 + - - -
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Residues in contact with VAL 6 (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 ARG* 1.3 80.0 - - - +
7A ASN* 1.3 72.8 + - - +
8A VAL* 5.2 0.4 - - + -
60A LEU* 4.7 9.2 - - + -
64A LEU* 5.5 0.9 - - + +
67A SER* 3.8 22.0 - - - +
68A LEU* 3.5 34.8 - - + -
69A PRO* 4.2 4.0 - - + -
85A LEU 3.3 4.8 + - - -
86A LEU* 3.7 7.1 - - + +
87A GLN* 2.9 25.8 + - - +
215A ILE* 3.8 26.7 - - + -
218A ARG* 4.1 8.3 - - - +
273A PHE* 5.0 1.1 - - - -
284A ASP* 5.8 2.5 - - - +
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Residues in contact with ASN 7 (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 ARG 4.3 0.2 - - - -
6A VAL* 1.3 75.1 - - - +
8A VAL* 1.3 59.2 + - - +
9A ASN* 3.0 21.5 - - - +
87A GLN* 3.1 33.8 + - - +
89A THR* 2.7 26.0 + - - +
218A ARG* 2.5 34.7 + - - +
273A PHE* 4.5 14.5 - - + -
283A GLY 3.5 15.9 - - - +
284A ASP* 4.7 13.0 + - - +
285A ARG* 4.0 14.3 - - - +
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Residues in contact with VAL 8 (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 ASN* 1.3 77.8 - - - +
9A ASN* 1.3 67.4 + - - +
10A VAL* 3.6 25.5 + - + -
86A LEU* 4.4 9.4 - - + -
87A GLN 2.9 9.1 + - - +
88A VAL* 3.3 6.3 - - + +
89A THR 2.9 24.6 + - - -
111A ASP* 4.1 17.7 - - + +
213A ILE* 3.7 34.1 - - + -
214A SER 4.9 0.7 - - - +
215A ILE* 3.9 24.7 - - + -
218A ARG* 4.6 2.0 - - - +
283A GLY 5.3 0.4 - - - -
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Residues in contact with ASN 9 (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 ASN* 3.0 22.0 + - - +
8A VAL* 1.3 74.9 - - - +
10A VAL* 1.3 62.9 + - - +
53A PHE* 5.2 1.2 - - - -
89A THR* 3.2 21.2 + - - +
91A VAL* 4.3 13.4 - - + +
109A ILE* 3.0 35.7 + - - +
110A ILE* 4.1 3.1 - - - -
111A ASP* 3.1 28.3 + - - +
218A ARG* 5.9 0.2 - - - +
244A THR* 3.3 30.7 + - - +
283A GLY 5.1 3.2 + - - -
285A ARG* 4.5 7.0 - - - +
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Residues in contact with VAL 10 (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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8A VAL* 3.6 7.0 - - + -
9A ASN* 1.3 78.5 - - - +
11A GLY* 1.3 70.9 + - - +
88A VAL* 4.1 15.5 - - + -
89A THR 2.9 14.5 + - - +
90A LEU* 3.4 14.7 - - + +
91A VAL* 3.0 20.4 + - - +
110A ILE* 4.1 1.6 - - - -
112A LEU* 3.6 28.3 - - + -
114A MET* 4.7 8.7 - - + -
209A LEU* 4.8 10.5 - - + -
213A ILE* 3.6 32.1 - - + -
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Residues in contact with GLY 11 (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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10A VAL* 1.3 79.6 - - - +
12A VAL* 1.3 62.1 + - - +
13A LEU* 4.0 4.0 - - - -
91A VAL* 3.5 10.8 - - - -
93A CYS* 5.6 0.7 - - - -
110A ILE* 3.5 27.0 - - - +
112A LEU 3.2 11.3 + - - -
113A MET* 3.8 0.2 - - - -
114A MET* 2.9 27.6 + - - +
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Residues in contact with VAL 12 (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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10A VAL 4.5 0.2 - - - +
11A GLY* 1.3 76.3 - - - -
13A LEU* 1.3 62.4 + - - +
20A LYS* 3.7 34.6 - - + +
23A LEU* 4.6 3.6 - - + -
24A ALA* 4.6 11.9 - - + -
90A LEU* 4.3 14.8 - - + -
91A VAL 3.1 11.9 + - - +
92A ASP* 4.2 14.6 - - - +
93A CYS* 3.1 26.7 + - - +
114A MET* 3.5 27.4 - - + -
116A VAL* 3.8 18.2 - - + -
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Residues in contact with LEU 13 (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 GLY* 4.0 8.3 - - - -
12A VAL* 1.3 88.5 - - - +
14A GLY* 1.3 58.6 + - - +
20A LYS* 3.5 7.6 - - - +
93A CYS* 4.0 14.8 - - - -
94A PRO 5.6 0.7 - - - -
103A ILE* 3.7 33.0 - - + +
107A ALA* 5.0 3.8 - - + -
110A ILE* 4.3 6.3 - - + -
113A MET* 3.7 40.2 - - + -
114A MET 2.9 10.9 + - - +
115A LEU* 4.3 2.0 - - + -
116A VAL* 2.9 31.0 + - - +
130A CYS* 3.9 21.8 - - + +
133A ILE* 4.8 8.1 - - + -
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Residues in contact with GLY 14 (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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13A LEU* 1.3 77.8 - - - +
15A HIS* 1.3 69.4 - - - +
18A SER* 4.0 2.5 - - - -
20A LYS* 3.6 9.0 + - - +
94A PRO 4.3 1.3 + - - +
95A GLY* 3.7 10.4 - - - -
103A ILE* 5.3 0.2 - - - +
115A LEU* 4.1 11.7 - - - -
116A VAL 3.7 14.4 - - - -
126A GLN* 4.4 2.7 - - - +
127A SER* 4.7 1.3 - - - -
130A CYS* 3.8 18.1 - - - -
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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