Contacts of the strand formed by residues 638 - 646 (chain A) in PDB entry 3VN4
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 PRO 638 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590A PRO* 3.6 34.4 - - + +
591A LEU* 4.1 22.9 - - + +
611A ILE* 3.8 34.8 - - + -
630A VAL* 4.0 9.0 - - + -
631A ALA 3.6 7.2 - - - +
632A LEU* 3.8 5.8 - - + -
633A THR* 4.7 1.8 - - - +
636A ARG 4.1 5.6 - - - +
637A LEU* 1.3 89.9 - - + +
639A ARG* 1.3 60.1 + - - +
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Residues in contact with ARG 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A HIS* 3.5 11.8 - - - +
590A PRO* 3.2 19.0 - - - +
631A ALA* 2.9 33.2 + - - +
632A LEU 4.3 11.9 + - - -
633A THR* 3.8 23.6 - - + +
637A LEU 3.2 0.6 + - - -
638A PRO* 1.3 74.1 - - - +
640A LEU* 1.3 84.3 + - + +
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Residues in contact with LEU 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584A TYR* 5.0 1.1 - - - +
586A ALA* 4.5 4.3 - - + -
587A ASN 3.6 16.6 - - - +
588A HIS* 3.5 36.1 - - + +
590A PRO* 4.6 0.9 - - - -
629A ARG 3.7 0.9 - - - +
630A VAL* 3.3 3.1 - - - -
631A ALA* 2.6 45.5 + - + +
638A PRO 3.9 0.2 - - - -
639A ARG* 1.3 106.8 - - + +
641A GLU* 1.3 72.8 + - - +
642A GLU* 3.8 28.0 - - + +
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Residues in contact with GLU 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586A ALA* 3.2 7.3 - - - +
587A ASN* 2.8 69.1 + - + +
590A PRO* 3.6 16.0 - - + +
594A HIS* 3.4 9.9 - - - +
595A LEU* 2.8 38.0 + - + -
611A ILE* 3.9 7.4 - - + +
628A TYR* 2.5 34.3 + - + +
629A ARG 3.6 3.6 - - - -
630A VAL* 4.3 4.0 - - + -
640A LEU* 1.3 74.9 - - - +
642A GLU* 1.3 63.9 + - - +
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Residues in contact with GLU 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A TYR* 2.5 41.9 + - + +
585A ILE 3.4 4.3 - - - +
586A ALA* 4.5 0.4 - - + -
627A GLU 3.5 1.7 - - - +
628A TYR* 3.4 4.5 - - - -
629A ARG* 2.8 52.2 + - + +
640A LEU* 3.8 24.8 - - + +
641A GLU* 1.3 80.7 - - - +
643A ILE* 1.3 64.4 - - - +
644A ARG* 4.9 10.8 + - + -
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Residues in contact with ILE 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A VAL 4.2 0.2 - - - +
584A TYR* 3.7 1.7 - - - -
585A ILE* 2.7 54.6 + - + +
595A LEU* 3.6 32.7 - - + +
597A VAL* 4.0 18.4 - - + -
626A VAL* 4.0 23.1 - - + -
627A GLU 3.4 2.9 - - - -
628A TYR* 3.7 20.2 - - + -
642A GLU* 1.3 76.0 - - - +
644A ARG* 1.3 70.1 + - - +
645A ILE* 4.3 11.0 - - + -
655A ILE* 3.9 24.7 - - + -
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Residues in contact with ARG 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583A VAL 3.7 6.8 + - - +
584A TYR* 3.8 35.7 - - + +
626A VAL* 3.7 0.2 - - - -
627A GLU* 2.8 46.2 + - + +
629A ARG* 6.5 0.9 - - - -
642A GLU* 4.9 10.7 + - + -
643A ILE* 1.3 79.9 - - - +
645A ILE* 1.3 62.8 + - - +
646A TRP* 3.6 39.5 - - + +
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Residues in contact with ILE 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546A GLN* 5.6 1.0 + - - -
576A VAL* 3.9 39.5 - - + -
582A SER* 5.0 4.7 + - - -
583A VAL* 3.3 39.1 + - + +
585A ILE* 5.2 0.2 - - + -
597A VAL* 6.2 0.4 - - + -
625A ARG 3.5 6.7 - - - +
626A VAL* 4.3 13.0 - - + -
643A ILE* 4.3 14.6 - - + -
644A ARG* 1.3 74.8 - - - +
646A TRP* 1.3 64.5 + - - +
647A GLY 3.8 17.7 + - - +
649A LEU* 3.9 29.4 - - + +
653A ALA* 5.1 1.8 - - + -
655A ILE* 4.9 7.6 - - + -
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Residues in contact with TRP 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514A ARG* 4.4 17.5 - - + -
516A ASP* 3.6 27.4 - - - -
623A ASP 4.4 1.6 - - - +
624A GLY* 3.3 1.9 - - - -
625A ARG* 2.9 69.9 + - + +
627A GLU* 3.2 38.5 + - + -
644A ARG* 3.6 46.3 - - + +
645A ILE* 1.3 74.3 - - - +
647A GLY* 1.3 68.5 + - - +
649A LEU* 4.7 0.5 - - - +
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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
------------------------------------------------------------
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