Contacts of the strand formed by residues 11 - 17 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C THR* 1.3 74.9 - - - +
12C THR* 1.3 66.5 + - - +
27D GLN* 3.7 13.0 - - - +
28D ASN* 4.2 5.6 - - + +
139D LYS* 3.6 7.1 - - - +
140D ILE* 2.8 40.5 + - + +
144D CYS* 3.8 35.7 - - + +
149D ILE* 4.8 2.5 - - + -
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Residues in contact with THR 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ALA* 1.3 81.0 + - - +
13C LEU* 1.3 62.5 + - - +
14C CYS* 4.0 21.8 - - - -
26D HIS* 3.1 8.3 - - - +
27D GLN* 3.0 45.3 + - - -
133D MET* 4.4 17.0 - - + +
137D CYS* 4.1 6.7 - - + -
138D PHE 3.4 11.0 - - - +
139D LYS* 5.2 2.1 - - - +
140D ILE* 5.0 1.3 - - - -
149D ILE* 4.9 0.7 - - - +
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Residues in contact with LEU 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C THR* 1.3 72.6 - - - +
14C CYS* 1.3 62.1 + - - +
15C LEU* 4.3 1.3 - - + -
24D PHE* 3.8 32.3 - - + -
25D ARG 3.2 16.6 - - - +
26D HIS* 4.0 10.1 - - + +
122D THR* 4.0 18.4 - - + -
126D LEU* 5.1 1.6 - - + -
136D GLY 4.1 0.2 - - - +
137D CYS* 3.0 2.4 - - - +
138D PHE* 2.7 43.7 + - + +
140D ILE* 4.3 10.2 - - + +
149D ILE* 4.2 22.0 - - + -
152D ILE* 3.9 33.4 - - + -
153D ARG* 5.3 2.0 - - + -
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Residues in contact with CYS 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C THR* 4.0 12.1 - - - -
13C LEU* 1.3 74.2 - - - +
15C LEU* 1.3 66.0 + - - +
14D TRP* 3.6 12.1 - - + -
24D PHE* 3.4 5.9 - - - +
25D ARG* 2.9 40.4 + - + +
136D GLY 3.5 3.8 - - - +
137D CYS* 2.0 46.9 - - - -
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Residues in contact with LEU 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LEU* 5.3 1.3 - - + -
14C CYS* 1.3 80.8 - - - +
16C GLY* 1.3 59.0 + - - +
10D ILE* 3.9 16.1 - - + +
14D TRP* 3.8 7.4 - - - -
23D GLY 3.4 3.1 - - - +
24D PHE* 3.8 16.6 - - + -
115D MET* 3.9 9.6 - - + -
118D LEU* 3.7 57.2 - - + +
119D PHE* 3.8 18.2 - - + +
122D THR* 4.0 8.5 - - + +
135D ASN 5.2 1.0 - - - +
136D GLY 2.9 16.8 + - - +
138D PHE* 3.6 34.5 - - + -
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Residues in contact with GLY 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LEU* 1.3 77.0 - - - +
17C HIS* 1.3 60.5 + - - -
10D ILE* 4.1 14.8 - - - -
12D ASN 5.5 0.4 - - - -
14D TRP* 3.6 20.3 - - - -
22D TYR* 3.4 4.0 - - - -
23D GLY 2.9 29.5 + - - +
115D MET* 3.6 12.4 - - - +
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Residues in contact with HIS 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C GLY* 1.3 74.3 - - - +
18C HIS* 1.3 71.5 + - - +
320C MET* 3.4 23.9 - - + -
321C ARG 4.7 2.2 + - - -
323C VAL* 4.4 12.1 - - + -
6D ILE* 3.5 41.7 - - + +
10D ILE* 3.8 27.3 + - + +
12D ASN 3.9 3.0 + - - -
13D GLY* 3.2 24.9 - - - -
14D TRP* 2.9 25.0 + - - +
17D MET* 5.0 2.7 - - - -
21D TRP 3.0 14.8 - - - +
22D TYR* 3.9 10.3 - - + +
23D GLY 4.9 0.2 - - - +
115D MET* 3.9 4.9 - - - -
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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