Contacts of the helix formed by residues 5 - 14 (chain K) in PDB entry 3J7Y
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 5 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4K PHE* 1.3 75.7 - - - +
6K ARG* 1.3 67.4 + - - +
8K PRO* 3.1 20.0 - - - +
9K GLN* 3.2 21.7 + - - +
227c GLU* 6.5 0.4 - - - -
229c PHE* 6.5 0.4 - - - -
230c GLU* 5.6 5.4 - - - -
295c GLU* 2.7 22.3 + - - +
298c ARG* 5.1 12.2 + - - -
302c ARG* 3.1 12.4 + - - +
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Residues in contact with ARG 6 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K SER* 1.3 73.6 - - - +
7K ALA* 1.3 62.0 + - - +
9K GLN* 3.2 7.5 + - - +
10K GLN* 2.9 29.3 + - - +
142a ARG* 3.0 50.9 + - - +
122b ASP* 4.2 13.7 + - - -
123b ASN* 5.8 0.2 + - - -
124b PRO* 6.1 0.6 - - - +
225c GLY* 3.9 23.4 + - - -
226c LYS* 5.7 0.2 - - - +
230c GLU* 4.5 20.9 + - - +
309c GLU* 5.5 7.0 + - - +
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Residues in contact with ALA 7 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K ARG* 1.3 74.6 - - - +
8K PRO* 1.3 68.9 - - + +
10K GLN* 3.2 19.9 + - - +
11K TRP* 2.9 27.6 + - - +
204T ARG* 4.7 16.7 - - - +
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Residues in contact with PRO 8 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K PHE* 5.3 0.2 - - + -
5K SER* 3.1 37.9 - - - +
6K ARG 3.5 2.0 - - - +
7K ALA* 1.3 96.3 - - + +
9K GLN* 1.3 54.3 + - - +
11K TRP* 3.2 9.2 + - + +
12K ALA 2.9 25.1 + - - -
285c PRO* 3.5 25.4 - - + +
286c GLY* 5.6 2.0 - - - +
291c VAL* 6.1 2.7 - - + -
295c GLU* 3.7 24.2 - - + -
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Residues in contact with GLN 9 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2K SER* 3.3 31.6 + - - +
3K SER 5.6 0.2 - - - +
4K PHE* 3.9 23.2 - - + -
5K SER 3.2 18.5 + - - +
6K ARG* 3.2 7.1 + - - +
8K PRO* 1.3 78.4 - - - +
10K GLN* 1.3 56.7 + - - +
12K ALA* 3.2 5.5 + - - +
13K THR* 2.9 21.5 + - - +
129b GLN* 3.2 43.3 + - + +
131b HIS* 4.0 20.2 + - - -
309c GLU* 6.1 1.3 - - - +
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Residues in contact with GLN 10 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K ARG 2.9 13.0 + - - +
7K ALA* 3.2 16.1 + - - +
9K GLN* 1.3 76.3 - - - +
11K TRP* 1.3 87.3 + - - +
13K THR* 3.2 13.7 + - + +
14K PHE* 2.9 42.1 + - + +
203T LEU 3.9 3.0 + - - -
204T ARG* 2.6 52.9 + - - +
206T ARG 3.7 14.8 - - - +
129b GLN* 4.5 2.9 - - - +
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Residues in contact with TRP 11 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K ALA 2.9 12.7 + - - +
8K PRO* 3.2 13.0 + - + +
10K GLN* 1.3 88.9 - - - +
12K ALA* 1.3 64.0 + - - +
14K PHE* 3.2 11.0 + - - -
15K ALA* 3.3 29.6 + - + +
200T ILE* 4.4 11.2 - - + -
203T LEU* 5.1 8.3 - - + -
204T ARG* 3.6 47.6 - - + -
267c LEU* 3.5 42.1 + - + -
268c PRO 2.9 27.4 + - - -
269c LEU* 3.9 12.1 - - + -
285c PRO* 6.0 0.2 - - + -
286c GLY* 4.9 7.9 - - - -
287c GLU* 4.2 23.3 - - + +
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Residues in contact with ALA 12 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8K PRO 2.9 12.4 + - - +
9K GLN* 3.4 17.9 - - - +
11K TRP* 1.3 77.8 - - - +
13K THR* 1.3 63.7 + - - +
14K PHE 3.4 2.6 - - - +
131b HIS* 3.4 6.8 - - + +
132b PRO* 3.1 21.7 - - - +
269c LEU* 3.7 16.7 - - - +
271c PHE* 4.0 18.4 - - + -
285c PRO* 3.8 21.5 - - + +
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Residues in contact with THR 13 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K GLN* 2.9 6.4 + - - +
10K GLN* 3.2 12.8 + - - +
12K ALA* 1.3 77.0 - - - +
14K PHE* 1.3 97.1 + - + +
44K LYS* 5.0 3.3 + - - +
46K VAL* 4.7 9.5 - - + +
208T ILE* 4.8 7.5 - - + +
129b GLN* 3.0 35.6 + - - +
130b TRP* 2.4 45.4 + - - -
131b HIS* 4.0 0.6 - - - +
132b PRO* 3.8 8.8 - - - +
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Residues in contact with PHE 14 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10K GLN* 2.9 38.0 + - + +
11K TRP* 3.2 1.7 + - - +
12K ALA 3.4 4.0 - - - +
13K THR* 1.3 104.9 - - + +
15K ALA* 1.3 78.9 + - - +
44K LYS* 4.1 9.1 + - + +
46K VAL* 3.4 27.6 - - + -
51K SER* 5.4 3.4 - - - -
53K CYS* 5.3 7.2 - - + +
206T ARG* 3.2 70.9 - - + +
207T THR* 3.4 29.8 - - - -
208T ILE* 4.3 2.2 - - + -
132b PRO* 4.0 5.7 - - - +
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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