Contacts of the strand formed by residues 638 - 644 (chain D) in PDB entry 1M7X
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 VAL 638 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504D HIS* 4.2 0.2 + - - -
630D VAL* 4.0 7.4 - - - +
633D ASP* 3.2 33.6 + - - +
636D ARG* 3.1 28.9 - - + +
637D SER* 1.3 76.6 - - - +
639D LEU* 1.3 65.1 + - - +
640D ILE* 4.2 11.9 - - + -
655D SER 3.3 9.9 - - - +
656D ASN* 3.8 19.3 - - - +
662D ARG* 4.4 5.4 - - + -
665D TYR* 3.9 18.4 - - + -
715D LEU* 3.4 29.8 - - + -
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Residues in contact with LEU 639 (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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492D TYR* 4.6 0.9 - - - +
504D HIS* 3.4 37.9 - - + +
507D LEU* 3.8 30.5 - - + -
508D THR* 3.8 18.2 - - + -
556D TRP* 3.7 32.4 - - + -
628D TRP* 4.4 6.1 - - + -
630D VAL 3.6 6.3 - - - +
631D VAL* 5.7 0.2 - - - -
637D SER 3.8 14.6 - - - +
638D VAL* 1.3 75.7 - - - +
640D ILE* 1.3 63.8 + - - +
653D VAL 3.9 1.4 - - - +
654D ALA* 3.5 0.7 - - - -
655D SER* 2.9 30.7 + - - -
657D PHE* 3.9 11.4 - - + -
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Residues in contact with ILE 640 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628D TRP* 3.9 2.4 - - - -
629D LEU* 2.8 26.9 + - + -
630D VAL* 2.9 28.9 + - + +
638D VAL* 4.2 10.1 - - + -
639D LEU* 1.3 79.9 - - - +
641D PHE* 1.3 67.1 + - - +
652D ILE* 3.8 23.3 - - + -
653D VAL 3.2 10.1 - - - +
654D ALA* 3.5 18.8 - - + -
665D TYR* 3.9 21.1 - - + -
667D PHE* 3.5 43.3 - - + -
715D LEU* 4.7 2.7 - - + -
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Residues in contact with PHE 641 (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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556D TRP* 3.6 33.0 - + - -
559D ALA* 3.8 31.4 - - + -
560D PHE* 4.1 11.2 - + + -
626D PHE* 3.2 32.8 - + + -
627D GLU 3.5 13.7 - - - +
628D TRP* 3.7 22.7 - + + -
629D LEU* 3.9 7.6 - - - +
640D ILE* 1.3 76.1 - - - +
642D VAL* 1.3 63.0 + - - +
643D ARG* 3.8 11.4 - - - -
652D ILE* 3.6 4.5 - - - +
653D VAL* 2.7 66.8 + - + +
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Residues in contact with VAL 642 (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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626D PHE* 3.5 6.1 - - - -
627D GLU* 3.1 33.4 + - + +
629D LEU* 4.5 11.0 - - + -
641D PHE* 1.3 79.2 - - - +
643D ARG* 1.3 69.9 + - - +
644D ARG* 4.1 22.9 - - - +
650D GLU* 3.4 40.2 - - + +
651D ILE 3.1 23.3 - - - +
652D ILE* 3.9 16.2 - - + +
670D ASN* 5.1 1.8 - - - +
675D TRP* 5.2 0.2 - - + -
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Residues in contact with ARG 643 (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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559D ALA 2.8 39.0 + - - +
560D PHE 3.9 1.4 + - - -
561D PRO* 3.8 16.3 - - - +
564D LYS* 5.4 0.2 - - - +
615D ALA* 2.9 38.8 + - - +
616D MET* 3.5 36.0 + - + +
619D LEU 3.8 8.3 + - - +
620D ASP* 2.5 51.1 + - - +
625D GLY 3.1 15.3 + - - -
626D PHE* 4.1 7.6 - - - -
641D PHE* 3.8 14.4 - - + -
642D VAL* 1.3 82.2 - - - +
644D ARG* 1.3 60.4 + - - +
650D GLU* 3.2 2.8 - - - -
651D ILE* 3.0 29.9 + - + -
653D VAL* 4.7 1.3 - - + -
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Residues in contact with ARG 644 (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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615D ALA* 3.9 7.3 + - - +
619D LEU* 3.7 10.4 + - - +
623D PRO 4.7 1.2 + - - -
624D TYR* 2.7 79.5 + - + +
625D GLY* 2.8 25.7 + - - +
626D PHE 4.9 1.1 + - - -
627D GLU* 2.6 42.4 + - - +
642D VAL* 4.1 5.2 - - + +
643D ARG* 1.3 75.6 - - - +
645D ASP* 1.3 72.6 + - - +
648D GLY 3.7 13.7 - - - +
649D ASN 3.2 10.1 - - - +
650D GLU* 2.7 31.6 + - + -
670D ASN* 3.8 1.8 - - - +
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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