Contacts of the helix formed by residues 630 - 641 (chain B) in PDB entry 1N1M
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 630 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547B TYR* 4.6 8.5 - - - -
629B TRP* 1.3 78.8 - - - +
631B TYR* 1.3 68.0 + - - -
633B GLY* 2.8 12.3 + - - -
634B TYR* 3.2 10.0 + - - +
653B VAL 2.9 13.9 + - - -
654B ALA 3.5 14.4 - - - -
655B PRO* 3.8 6.3 - - - +
656B VAL 4.2 0.8 + - - -
740B HIS* 2.6 30.2 + - - -
955B A3M 2.9 28.4 + - - -
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Residues in contact with TYR 631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547B TYR* 3.1 36.9 - - + +
548B ALA 3.6 7.4 - - - -
549B GLY* 3.4 5.2 - - - -
550B PRO* 3.5 20.8 - - + +
594B ILE* 4.8 0.2 - - - +
598B LEU* 3.2 18.1 - - + +
602B GLU* 2.4 40.4 + - - -
629B TRP 3.2 0.2 + - - -
630B SER* 1.3 82.8 + - - +
632B GLY* 1.3 56.6 + - - +
634B TYR* 3.4 11.9 + + - +
635B VAL* 3.1 30.9 + - + +
659B TRP* 3.6 33.0 - + - -
666B TYR* 3.3 18.8 - - - -
955B A3M 3.4 13.1 - - + +
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Residues in contact with GLY 632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546B VAL* 3.5 26.1 - - - +
547B TYR* 3.5 14.7 + - - +
628B GLY 3.5 6.1 - - - -
629B TRP 2.9 9.8 + - - -
631B TYR* 1.3 77.0 - - - +
633B GLY* 1.3 56.5 + - - +
635B VAL* 4.4 0.9 - - - -
636B THR* 2.6 38.9 + - - -
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Residues in contact with GLY 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628B GLY 3.3 21.7 - - - -
629B TRP 3.5 1.0 - - - +
630B SER 2.8 8.6 + - - -
632B GLY* 1.3 77.6 - - - +
634B TYR* 1.3 56.1 + - - +
636B THR* 3.2 3.4 + - - -
637B SER* 2.9 32.9 + - - -
652B ALA* 3.8 9.2 - - - +
653B VAL 4.2 2.5 - - - -
655B PRO* 3.4 17.5 - - - -
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Residues in contact with TYR 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599B GLY* 3.2 33.0 - - - -
602B GLU* 4.2 2.2 - - - -
630B SER 3.2 6.7 + - - +
631B TYR* 3.5 26.2 - + - +
633B GLY* 1.3 75.0 - - - +
635B VAL* 1.3 67.0 + - + +
637B SER* 3.1 5.7 + - - -
638B MET* 3.0 47.4 + - + +
655B PRO* 3.5 3.3 - - - +
656B VAL* 3.0 48.9 - - + +
657B SER 4.4 4.3 - - - -
659B TRP* 3.4 36.2 + + - -
686B SER* 3.0 29.6 + - - -
688B VAL* 4.0 6.1 - - + -
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Residues in contact with VAL 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546B VAL* 3.9 21.8 - - + -
547B TYR 3.7 7.0 - - - +
548B ALA* 4.1 5.6 - - + -
602B GLU* 3.8 15.5 - - - +
603B VAL* 4.1 23.3 - - + -
606B GLN* 4.4 8.5 - - + -
631B TYR* 3.1 43.1 + - + +
632B GLY 4.0 2.9 - - - +
634B TYR* 1.3 83.7 - - + +
636B THR* 1.3 65.1 + - - +
638B MET* 3.3 6.3 + - - +
639B VAL* 3.0 26.8 + - + +
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Residues in contact with THR 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546B VAL* 2.9 19.9 - - - +
626B ILE* 3.5 30.3 - - + +
627B TRP* 3.2 8.5 - - - -
628B GLY 4.1 0.2 - - - -
632B GLY 2.6 25.0 + - - -
633B GLY 3.4 4.9 - - - +
635B VAL* 1.3 78.5 - - - +
637B SER* 1.3 58.0 + - - +
639B VAL* 3.7 2.6 - - - +
640B LEU* 3.0 38.9 + - + +
651B ILE 3.4 29.2 - - - +
652B ALA* 4.6 1.1 - - + -
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Residues in contact with SER 637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633B GLY 2.9 15.5 + - - -
634B TYR 3.5 6.7 - - - -
636B THR* 1.3 73.2 - - - +
638B MET* 1.3 61.8 + - - +
640B LEU* 3.0 9.6 + - - +
641B GLY* 2.8 26.7 + - - -
652B ALA* 3.6 6.8 - - - +
655B PRO* 4.2 5.0 - - - +
688B VAL* 3.7 29.8 - - - +
695B PHE* 3.4 12.4 - - - -
700B TYR* 3.0 21.9 + - - -
719B ILE* 4.5 0.3 - - - +
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Residues in contact with MET 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599B GLY* 3.7 18.8 - - - +
603B VAL* 3.9 15.7 - - + -
634B TYR* 3.0 59.3 + - + +
635B VAL 3.6 6.5 - - - +
637B SER* 1.3 75.3 - - - +
639B VAL* 1.3 61.1 + - - +
641B GLY 3.2 2.4 + - - -
642B SER* 3.2 12.1 + - - -
686B SER* 3.9 14.6 - - - +
687B THR 3.5 22.0 - - - +
688B VAL* 4.1 6.1 - - + -
691B ARG* 3.1 52.9 + - - +
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Residues in contact with VAL 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603B VAL* 3.4 35.9 - - + +
606B GLN* 4.5 3.4 - - + -
607B ILE* 3.8 9.9 - - + -
626B ILE* 3.9 18.8 - - + -
635B VAL* 3.0 23.7 + - + +
636B THR 3.7 4.3 - - - +
638B MET* 1.3 73.9 - - - +
640B LEU* 1.3 65.0 + - - +
642B SER* 2.6 27.6 + - - -
644B SER* 4.6 0.2 + - - -
647B PHE* 3.3 43.3 - - + -
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Residues in contact with LEU 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626B ILE* 4.0 11.9 - - + -
636B THR* 3.0 22.6 + - + +
637B SER 3.0 8.1 + - - +
639B VAL* 1.3 76.6 - - - +
641B GLY* 1.3 56.1 + - - +
642B SER 3.3 2.5 + - - -
643B GLY 4.5 3.6 + - - -
647B PHE* 4.4 8.3 - - + -
649B CYS 3.9 23.1 - - - +
650B GLY* 3.7 19.7 - - - +
694B ASN 4.2 8.0 - - - +
695B PHE* 3.7 12.7 - - + -
697B GLN* 5.7 0.2 - - - +
698B VAL* 4.0 43.8 - - + +
700B TYR* 3.3 38.4 - - + -
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Residues in contact with GLY 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637B SER 2.8 12.6 + - - -
638B MET 3.4 7.2 - - - -
639B VAL 3.1 0.2 - - - -
640B LEU* 1.3 77.6 - - - +
642B SER* 1.3 58.4 + - - +
643B GLY 3.5 2.2 - - - -
691B ARG* 3.2 30.3 - - - +
694B ASN* 3.5 19.8 - - - +
695B PHE* 3.8 18.1 - - - -
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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