Contacts of the strand formed by residues 2 - 8 (chain D) in PDB entry 6AVO
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 THR 2 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D THR* 1.3 71.9 + - - +
3D THR* 1.3 66.3 + - - +
17D ASP* 2.9 36.0 + - - +
127D SER* 4.2 0.9 - - - +
128D THR 3.8 4.0 - - - +
131D GLY* 3.0 45.0 + - - +
132D ASN* 4.0 4.0 - - - -
135D ALA* 3.9 14.8 - - + -
160D ILE* 3.8 12.9 - - + +
163D ALA* 3.7 21.8 + - + +
164D THR* 5.0 2.0 - - - -
167D ASP* 3.9 0.5 + - - -
170D SER* 3.4 8.3 + - - -
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Residues in contact with THR 3 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D THR* 3.7 9.8 - - - +
2D THR* 1.3 78.5 + - - +
4D LEU* 1.3 60.4 + - - +
15D ALA 3.6 4.0 - - - +
16D VAL* 3.2 33.6 - - + +
33D LYS* 4.7 0.3 - - - +
44D THR* 3.3 16.6 - - + +
45D MET 3.6 14.8 + - - -
100D MET* 3.2 23.5 - - + +
127D SER* 3.0 2.0 - - - -
128D THR* 2.5 51.6 + - - -
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Residues in contact with LEU 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D THR* 1.3 76.0 - - - +
5D ALA* 1.3 67.0 + - - +
6D PHE* 4.0 16.8 - - + -
13D ILE* 4.8 1.8 - - + -
14D ALA* 3.5 1.9 - - - +
15D ALA* 2.9 41.5 + - + +
100D MET* 4.1 5.4 - - - +
126D PHE 3.2 15.9 - - - +
127D SER* 3.7 7.2 - - - +
135D ALA* 3.5 13.2 - - + -
139D MET* 3.4 23.3 - - + -
156D GLY* 5.0 1.8 - - - -
159D ALA* 3.2 33.4 - - + -
160D ILE* 3.3 26.2 - - + -
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Residues in contact with ALA 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 1.3 82.9 - - - +
6D PHE* 1.3 61.9 + - - +
12D VAL* 4.7 0.7 - - + -
13D ILE 3.4 13.0 - - - +
14D ALA* 3.9 13.9 - - + -
100D MET* 4.4 11.7 - - + -
102D CYS* 4.1 16.4 - - - -
111D LEU* 3.8 15.6 - - + +
124D ASN 3.7 0.5 - - - +
125D MET* 3.5 0.3 - - - -
126D PHE 2.7 37.0 + - - +
139D MET* 4.7 0.2 - - - -
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Residues in contact with PHE 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 4.0 8.7 - - + -
5D ALA* 1.3 74.6 - - - +
7D LYS* 1.3 60.4 + - - +
8D PHE* 3.6 24.6 - + - -
12D VAL* 3.3 6.6 - - - +
13D ILE* 3.2 61.7 + - + -
111D LEU* 4.5 1.3 - - - -
124D ASN 2.9 13.2 - - - +
125D MET* 4.0 9.2 - - + -
139D MET* 3.3 31.9 - - + -
143D TYR* 3.5 25.4 - + + -
147D LEU* 5.0 2.7 - - + -
152D ALA* 3.9 23.3 - - + -
155D LEU* 4.5 14.4 - - + -
156D GLY* 4.7 5.4 - - - -
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Residues in contact with LYS 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D PHE* 1.3 75.2 - - - +
8D PHE* 1.3 61.3 + - - +
11D GLY 3.2 5.6 - - - +
12D VAL* 3.2 26.5 - - + -
109D PRO* 2.6 39.5 + - + +
110D GLY* 4.4 1.4 - - - -
111D LEU* 4.3 10.9 - - + +
122D SER* 4.7 7.9 + - - -
123D GLY 3.5 20.3 + - - +
124D ASN* 3.1 31.1 + - - +
143D TYR* 2.5 29.3 + - - -
145D PRO* 5.5 0.3 - - - +
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Residues in contact with PHE 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D PHE* 3.6 23.6 - + + -
7D LYS* 1.3 77.3 - - - +
9D GLN* 1.3 80.7 + - - +
10D HIS* 3.1 31.1 + + + -
11D GLY 3.0 19.1 + - - +
13D ILE* 3.9 17.3 - - + -
109D PRO* 5.3 5.4 - - - +
143D TYR* 4.4 9.2 - - + +
144D ARG 5.1 0.7 - - - +
145D PRO* 3.9 20.0 - - + +
147D LEU* 3.2 28.7 - - + +
148D SER 4.4 0.2 - - - -
149D PRO* 4.4 7.9 - - + -
152D ALA* 3.8 25.6 - - + -
178D HIS* 4.0 19.3 - - - -
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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