Contacts of the helix formed by residues 10 - 15 (chain B) in PDB entry 7D1M
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 10 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A PRO* 3.3 6.9 - - - +
10A SER* 3.0 19.5 + - - -
8B PHE 3.2 1.9 + - - -
9B PRO* 1.3 71.4 - - - +
11B GLY* 1.3 65.0 + - - +
12B LYS 3.3 2.5 - - - -
13B VAL* 3.0 7.5 + - - +
14B GLU* 2.7 41.3 + - - +
115B LEU* 3.9 21.3 - - - -
125B VAL* 4.3 17.4 - - - +
150B PHE* 4.2 11.9 - - - -
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Residues in contact with GLY 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLY* 3.6 13.2 - - - -
14A GLU* 2.8 28.3 + - - -
9B PRO 3.5 1.0 - - - -
10B SER* 1.3 70.8 - - - +
12B LYS* 1.3 62.3 + - - +
13B VAL 3.2 0.5 + - - -
14B GLU* 3.2 14.2 + - - +
15B GLY* 3.2 19.1 + - - -
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Residues in contact with LYS 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU* 4.4 9.2 + - - +
9B PRO 4.8 1.2 + - - -
10B SER 3.3 1.0 - - - -
11B GLY* 1.3 76.3 - - - +
13B VAL* 1.3 61.0 + - + +
15B GLY* 4.0 3.1 + - - -
16B CYS* 3.5 20.1 - - - -
97B LYS 4.5 3.3 - - - +
99B PRO* 3.9 21.1 - - + +
152B ILE* 4.7 15.9 - - + +
154B TYR 5.3 0.7 - - - -
155B ASP 3.7 17.3 - - - +
157B VAL* 3.9 29.4 - - + -
305B PHE* 4.5 3.8 + - - +
306B GLN* 3.2 49.3 + - - +
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Residues in contact with VAL 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B SER 3.0 8.1 + - - +
12B LYS* 1.3 76.8 - - + +
14B GLU* 1.3 65.9 + - - +
15B GLY 3.1 1.8 - - - -
16B CYS* 2.9 20.1 + - - +
17B MET* 3.5 11.7 - - - +
30B LEU* 4.7 0.7 - - + -
115B LEU* 3.9 16.2 - - + -
148B VAL* 3.7 28.9 - - + -
150B PHE* 3.8 43.5 - - + -
152B ILE* 5.5 0.2 - - + -
157B VAL* 4.0 10.3 - - + -
159B PHE* 3.9 17.5 - - + -
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Residues in contact with GLU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PRO* 3.4 16.2 - - + +
10A SER 3.2 1.2 + - - -
11A GLY* 2.7 33.9 + - - -
12A LYS* 4.4 10.6 + - - +
10B SER* 2.7 38.4 + - - +
11B GLY* 3.2 6.3 + - - +
13B VAL* 1.3 75.8 - - - +
15B GLY* 1.3 58.3 + - - +
16B CYS 3.1 4.5 + - - -
17B MET* 3.2 17.8 + - - +
115B LEU* 3.8 20.8 - - + +
122B PRO* 3.9 21.2 - - + +
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Residues in contact with GLY 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLY 3.2 10.5 + - - -
12B LYS 4.0 2.4 + - - -
13B VAL 3.1 1.4 - - - -
14B GLU* 1.3 77.4 - - - +
16B CYS* 1.3 60.1 - - - +
17B MET 3.6 1.3 - - - -
31B TRP* 4.9 3.3 - - - -
95B ASN* 3.0 18.7 + - - +
97B LYS* 3.7 34.8 - - - +
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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