Contacts of the strand formed by residues 259 - 262 (chain 4) in PDB entry 3EXG
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 LEU 259 (chain 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2074 ILE* 4.1 0.6 - - - +
2084 THR* 3.5 20.4 - - + +
2104 VAL* 3.7 27.4 - - + -
2494 ILE* 4.5 2.0 - - + -
2534 VAL* 4.0 12.8 - - + -
2584 HIS* 1.3 78.9 - - - +
2604 VAL* 1.3 83.3 + - - +
2614 THR* 4.6 5.6 - - + +
2754 ILE* 4.5 14.1 - - + +
2764 CYS* 5.5 1.3 - - - -
2794 ILE* 3.5 34.3 - - + -
2884 LEU* 4.5 6.3 - - + +
2904 ALA 5.3 0.6 + - - -
2914 PRO 4.6 0.7 - - - +
2924 ALA* 3.4 45.1 - - + +
2934 VAL* 3.4 2.3 + - - +
3264 THR* 4.6 4.0 + - - +
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Residues in contact with VAL 260 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2074 ILE* 4.1 16.6 - - + -
2084 THR 2.6 13.1 + - - +
2094 VAL* 3.2 16.9 - - + +
2104 VAL 2.9 24.4 + - - -
2594 LEU* 1.3 80.6 - - - +
2614 THR* 1.3 76.0 + - - +
2624 VAL* 4.1 8.1 - - + -
2934 VAL* 3.3 24.7 - - + +
2954 VAL* 3.8 19.1 - - + -
3194 ILE* 5.4 1.6 - - + +
3224 ALA* 4.1 12.8 - - + +
3234 ILE* 4.6 7.4 - - + -
3264 THR* 4.2 2.0 - - - +
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Residues in contact with THR 261 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2104 VAL* 3.5 11.7 - - + -
2594 LEU* 4.3 8.5 - - + -
2604 VAL* 1.3 81.2 - - - +
2624 VAL* 1.3 61.3 + - - +
2634 GLU* 5.1 1.2 + - - -
2724 GLY* 3.7 17.2 - - - +
2754 ILE* 3.8 43.5 - - + -
2764 CYS* 5.0 5.8 - - - -
2924 ALA* 6.2 0.2 - - + -
2934 VAL 3.3 4.4 + - - +
2944 ARG* 3.5 26.2 - - - +
2954 VAL 2.9 26.5 + - - -
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Residues in contact with VAL 262 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2094 VAL* 3.8 15.9 - - + -
2104 VAL 2.8 8.7 + - - +
2114 SER* 2.5 43.7 + - - +
2124 HIS* 4.0 1.7 + - - -
2154 PRO* 3.8 16.2 - - + -
2194 CYS* 3.7 24.2 - - - -
2384 MET* 5.3 0.9 - - - +
2604 VAL* 4.1 7.6 - - + -
2614 THR* 1.3 79.1 - - - +
2634 GLU* 1.3 64.6 + - - +
2954 VAL* 3.2 10.1 - - + +
3144 PRO* 4.7 6.5 - - + -
3194 ILE* 4.0 28.3 - - + -
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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