Contacts of the helix formed by residues 636 - 652 (chain D) in PDB entry 3TMH
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 TRP 636 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B GLN* 3.1 42.0 - - + -
15B GLY* 5.7 1.3 - - - -
18B VAL* 3.3 42.2 - - + -
635D ALA* 1.3 76.5 - - - +
637D LYS* 1.3 62.7 + - - +
638D ILE* 3.0 4.9 - - - +
639D ALA* 2.4 31.9 + - + +
640D LYS* 2.9 12.1 + - - +
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Residues in contact with LYS 637 (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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635D ALA 3.3 3.9 + - - +
636D TRP* 1.3 79.1 - - - +
638D ILE* 1.3 63.4 + - - +
640D LYS* 2.9 36.0 + - - +
641D MET 3.0 1.0 + - - -
641L MET* 3.1 22.6 - - + +
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Residues in contact with ILE 638 (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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21B LEU* 4.0 5.6 - - + -
5C ILE* 4.1 21.1 - - + -
635D ALA* 3.2 39.9 - - + +
637D LYS* 1.3 78.9 - - - +
639D ALA* 1.3 64.6 + - - +
641D MET* 2.6 45.3 + - - +
642D ILE* 2.9 37.7 + - + -
641L MET* 3.3 12.1 - - + +
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Residues in contact with ALA 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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14B GLN* 4.8 7.6 - - + +
17B THR* 4.0 28.8 - - + +
18B VAL* 4.5 6.5 - - + +
21B LEU* 4.6 4.0 - - + -
636D TRP* 2.4 45.8 + - + +
638D ILE* 1.3 75.8 - - + +
640D LYS* 1.3 59.9 + - - +
642D ILE* 3.2 8.8 - - - +
643D VAL* 3.0 27.0 + - - +
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Residues in contact with LYS 640 (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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10B THR* 6.0 5.8 - - + -
14B GLN* 4.9 16.4 - - - +
636D TRP 2.9 7.3 + - - +
637D LYS* 2.9 33.0 - - - +
639D ALA* 1.3 75.0 - - - +
641D MET* 1.3 94.9 + - - +
643D VAL* 2.8 18.6 + - - +
644D SER* 2.9 25.9 + - - +
640L LYS* 4.3 15.2 - - - +
641L MET* 4.0 7.6 - - - +
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Residues in contact with MET 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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638D ILE* 2.6 28.4 + - - +
640D LYS* 1.3 93.9 - - - +
642D ILE* 1.3 66.7 + - + +
644D SER* 3.0 2.3 + - - -
645D ASP* 3.0 28.0 + - + +
637L LYS* 2.9 52.7 - - + +
638L ILE* 3.4 6.3 - - - +
640L LYS* 3.5 10.3 - - - +
641L MET* 3.0 50.3 - - + -
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Residues in contact with ILE 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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17B THR* 4.3 13.2 - - + -
21B LEU* 5.2 2.7 - - + -
5C ILE* 4.5 21.1 - - + -
9C LEU* 4.8 10.3 - - + -
10C THR* 4.4 13.7 - - - +
13C LEU* 4.5 14.8 - - + -
638D ILE* 3.5 36.6 - - + +
639D ALA* 3.2 13.9 - - - +
641D MET* 1.3 84.3 - - + +
643D VAL* 1.3 68.1 + - + +
645D ASP* 3.6 7.1 - - - +
646D VAL* 2.9 36.6 + - + +
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Residues in contact with VAL 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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10B THR* 4.0 28.5 - - + +
13B LEU* 3.5 47.8 - - + -
14B GLN* 4.1 15.3 - - + +
17B THR* 4.3 8.7 - - - +
13C LEU* 5.2 1.3 - - + -
639D ALA 3.1 17.9 - - - +
640D LYS* 2.8 12.2 + - - +
642D ILE* 1.3 73.2 - - + +
644D SER* 1.3 64.1 + - - +
646D VAL* 2.9 25.6 - - - +
647D MET* 2.9 13.7 + - + +
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Residues in contact with SER 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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10B THR* 5.4 5.5 - - - +
640D LYS* 2.9 32.4 + - - +
641D MET* 3.0 11.4 + - - -
643D VAL* 1.3 73.2 - - - +
645D ASP* 1.3 55.4 + - - +
647D MET* 2.9 33.7 + - - +
648D GLN* 3.0 11.5 + - - +
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Residues in contact with ASP 645 (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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10C THR* 4.2 15.1 + - - +
641D MET* 3.0 22.8 + - + +
642D ILE* 3.6 7.5 - - - +
644D SER* 1.3 72.4 + - - +
646D VAL* 1.3 70.9 + - - +
648D GLN* 3.5 22.3 + - - +
649D GLN* 2.9 47.1 + - - +
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Residues in contact with VAL 646 (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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13B LEU* 4.9 3.6 - - + -
10C THR* 3.9 25.1 - - + +
13C LEU* 4.4 17.5 - - + -
14C GLN* 4.3 22.0 - - + +
17C THR* 4.3 21.3 - - + +
642D ILE* 2.9 32.2 + - + +
643D VAL* 2.9 13.2 - - - +
645D ASP* 1.3 73.4 + - - +
647D MET* 1.3 72.4 + - - +
649D GLN* 2.8 20.3 + - - +
650D ALA* 2.9 12.6 + - + +
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Residues in contact with MET 647 (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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9B LEU* 3.3 43.3 - - + -
10B THR* 3.5 29.2 - - - +
13B LEU* 4.4 9.2 - - + -
17C THR* 4.1 11.7 - - - -
21C LEU* 6.4 0.2 - - - -
643D VAL* 2.9 16.6 + - + +
644D SER* 2.9 22.9 + - - +
646D VAL* 1.3 75.4 - - - +
648D GLN* 1.3 54.7 + - - +
650D ALA* 2.7 29.5 + - - +
651D GLN* 3.0 13.7 + - - +
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Residues in contact with GLN 648 (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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644D SER 3.5 12.1 - - - +
645D ASP* 3.5 26.0 + - - +
647D MET* 1.3 77.1 - - - +
649D GLN* 1.3 69.8 + - - +
651D GLN* 3.2 38.7 - - - +
652D TYR* 3.2 14.9 + - - +
427E ASN* 4.2 25.6 - - - +
428E GLY* 5.4 1.6 - - - -
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Residues in contact with GLN 649 (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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10C THR* 5.7 3.4 - - + -
14C GLN* 4.5 16.8 - - - +
645D ASP* 2.9 41.8 + - - +
646D VAL* 2.8 18.0 + - - +
648D GLN* 1.3 82.0 - - - +
650D ALA* 1.3 58.6 + - - +
652D TYR* 4.1 5.6 - - - +
653D ASP* 3.1 26.3 + - - +
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Residues in contact with ALA 650 (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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14C GLN* 5.2 10.1 - - + +
17C THR* 4.6 18.6 - - + -
18C VAL* 5.1 18.5 - - + +
21C LEU* 4.7 12.1 - - + -
646D VAL* 2.9 8.4 + - + +
647D MET* 2.7 19.8 + - - +
649D GLN* 1.3 69.3 - - - +
651D GLN* 1.3 66.7 + - - +
652D TYR 3.1 2.2 - - - -
653D ASP* 2.8 27.8 + - - +
654D GLN 4.2 2.1 - - - +
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Residues in contact with GLN 651 (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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21C LEU* 5.3 8.7 - - + +
647D MET 3.0 6.3 + - - +
648D GLN* 3.2 41.1 + - - +
650D ALA* 1.3 76.1 - - - +
652D TYR* 1.3 58.6 + - + +
653D ASP 3.1 4.5 + - - -
654D GLN* 3.3 18.7 + - - +
655D PRO* 5.0 1.9 - - - +
425E GLU* 5.3 5.5 - - - +
428E GLY* 3.9 26.3 + - - +
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Residues in contact with TYR 652 (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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648D GLN 3.2 15.7 + - - +
649D GLN* 4.1 7.4 - - - +
650D ALA 3.1 1.0 - - - -
651D GLN* 1.3 77.5 - - + +
653D ASP* 1.3 58.3 + - - +
654D GLN* 2.9 15.2 + - - -
378E LEU* 3.1 37.7 - - + +
428E GLY* 6.2 4.0 - - - -
451E THR* 5.6 5.6 - - + -
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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