Contacts of the strand formed by residues 11 - 17 (chain A) in PDB entry 5HMG
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 ALA 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A THR* 1.3 74.5 - - - +
12A THR* 1.3 66.2 + - - +
27B GLN 4.0 11.2 - - - +
28B ASN* 4.9 3.4 - - - +
29B SER* 5.3 0.2 - - - +
139B LYS* 3.6 6.9 - - - +
140B ILE* 2.8 41.1 + - + +
144B CYS* 3.8 36.8 - - + +
149B ILE* 4.8 4.7 - - + -
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Residues in contact with THR 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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11A ALA* 1.3 80.3 + - - +
13A LEU* 1.3 61.6 + - - +
14A CYS* 4.1 18.6 - - - -
26B HIS* 3.1 9.9 - - - +
27B GLN* 3.1 43.4 + - - +
133B MET* 4.0 27.4 - - + +
137B CYS* 4.1 0.4 - - + -
138B PHE 3.4 11.2 - - - +
139B LYS* 5.4 0.7 - - - +
140B ILE* 5.0 1.3 - - - -
149B ILE* 5.0 0.6 - - - +
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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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12A THR* 1.3 72.9 - - - +
14A CYS* 1.3 59.6 + - - +
15A LEU* 5.3 0.7 - - + -
24B PHE* 3.8 32.3 - - + -
25B ARG 3.5 15.0 - - - +
26B HIS* 4.2 9.9 - - + -
122B THR* 4.0 18.8 - - + -
126B LEU* 5.1 1.8 - - + -
136B GLY 4.1 0.3 - - - +
137B CYS* 3.0 3.3 - - - +
138B PHE* 2.7 43.0 + - + +
140B ILE* 4.3 10.4 - - + +
149B ILE* 4.2 23.6 - - + -
152B ILE* 3.9 33.0 - - + -
153B ARG* 5.3 1.8 - - + -
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Residues in contact with CYS 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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12A THR* 4.1 11.4 - - - -
13A LEU* 1.3 76.1 - - - +
15A LEU* 1.3 65.7 + - - +
14B TRP* 3.5 14.1 - - + -
24B PHE* 3.4 5.7 - - - +
25B ARG* 2.9 36.9 + - + +
26B HIS* 6.2 0.2 - - - -
136B GLY 3.5 4.0 - - - +
137B CYS* 2.0 47.3 - - - -
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Residues in contact with LEU 15 (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* 5.3 1.1 - - + -
14A CYS* 1.3 80.9 - - - +
16A GLY* 1.3 59.8 + - - +
10B ILE* 3.9 15.5 - - + +
14B TRP* 3.8 6.3 - - - -
23B GLY 3.4 4.3 - - - +
24B PHE* 3.8 16.6 - - + -
115B MET* 3.8 9.6 - - + -
118B LEU* 3.7 42.4 - - + +
119B PHE* 3.8 33.4 - - + +
122B THR* 4.0 9.2 - - + +
135B ASN 5.2 0.7 - - - +
136B GLY* 2.9 18.2 + - - +
138B PHE* 3.6 33.7 - - + -
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Residues in contact with GLY 16 (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 LEU* 1.3 77.6 - - - +
17A HIS* 1.3 59.7 + - - -
10B ILE* 4.1 15.3 - - - -
12B ASN 5.5 0.4 - - - -
14B TRP* 3.6 20.1 - - - -
22B TYR* 3.4 3.6 - - - -
23B GLY 3.0 30.0 + - - +
115B MET* 3.6 12.1 - - - +
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Residues in contact with HIS 17 (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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16A GLY* 1.3 73.9 - - - +
18A HIS* 1.3 71.8 + - - +
320A MET* 3.5 23.7 - - + -
321A ARG 4.7 2.7 + - - -
323A VAL* 4.4 11.7 - - + -
6B ILE* 3.5 41.6 - - + +
7B ALA 4.5 0.4 + - - -
10B ILE* 3.7 26.9 + - + +
12B ASN 3.9 4.5 + - - -
13B GLY* 3.2 23.9 - - - -
14B TRP* 3.0 24.7 + - - -
17B MET* 5.0 2.7 - - - -
21B TRP 3.0 14.1 - - - +
22B TYR* 3.9 11.0 - - + +
115B MET* 4.0 5.2 - - - -
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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