Contacts of the helix formed by residues 623 - 634 (chain B) in PDB entry 4G3D
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 ALA 623 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489B GLU* 2.9 18.8 + - - +
621B SER 3.9 0.2 + - - -
622B CYS* 1.3 73.5 - - - +
624B PRO* 1.3 75.1 - - + +
626B THR* 3.0 13.6 + - - +
627B ALA* 2.9 21.0 + - - +
654B ALA* 5.3 0.7 - - + +
657B GLN* 3.9 18.6 - - + +
658B VAL* 3.7 18.8 - - + -
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Residues in contact with PRO 624 (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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622B CYS 3.7 3.1 - - - +
623B ALA* 1.3 82.6 - - - +
625B LEU* 1.3 49.8 + - - +
627B ALA* 3.3 9.4 + - + +
628B GLN* 2.8 36.4 + - - +
657B GLN* 3.4 22.2 - - - +
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Residues in contact with LEU 625 (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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623B ALA 3.2 0.6 - - - -
624B PRO* 1.3 77.3 - - - +
626B THR* 1.3 64.4 + - - +
628B GLN* 3.8 17.7 - - + +
629B ALA* 3.1 21.3 + - - +
650B LYS* 3.7 32.3 - - + +
653B ARG* 4.0 52.3 - - + +
654B ALA* 4.1 6.6 - - + +
657B GLN* 2.8 27.7 + - + +
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Residues in contact with THR 626 (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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489B GLU* 2.8 31.9 + - + +
493B LEU* 3.5 33.8 - - + +
586B MET* 4.0 9.2 - - + -
622B CYS* 4.4 9.0 - - + -
623B ALA* 3.0 14.0 + - - +
625B LEU* 1.3 76.4 - - - +
627B ALA* 1.3 65.7 + - - +
629B ALA* 3.4 4.9 + - - +
630B ILE* 3.1 44.4 + - + +
654B ALA* 3.7 8.6 - - - +
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Residues in contact with ALA 627 (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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618B ILE* 3.7 32.6 - - + +
622B CYS* 4.8 3.9 - - + +
623B ALA 2.9 12.0 + - - +
624B PRO* 3.4 12.6 - - + +
626B THR* 1.3 78.6 - - - +
628B GLN* 1.3 56.0 + - - +
630B ILE* 3.3 3.2 + - - +
631B GLN* 2.9 38.3 + - - +
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Residues in contact with GLN 628 (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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624B PRO 2.8 21.2 + - - +
625B LEU* 4.0 19.5 - - + +
626B THR 3.3 0.2 - - - -
627B ALA* 1.3 69.9 - - - +
629B ALA* 1.3 61.1 + - - +
631B GLN* 3.3 15.3 + - + +
632B GLU* 2.9 55.6 + - + +
650B LYS* 4.9 8.6 - - + +
653B ARG* 5.5 3.1 + - - -
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Residues in contact with ALA 629 (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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493B LEU* 6.0 0.9 - - + -
496B LEU* 6.2 0.7 - - + -
625B LEU* 3.1 18.1 + - - +
626B THR* 3.4 6.3 + - - +
628B GLN* 1.3 75.7 - - - +
630B ILE* 1.3 63.7 + - + +
632B GLU* 3.1 4.9 + - - -
633B GLY* 2.9 19.8 + - - -
647B LEU* 3.3 28.8 - - + +
650B LYS* 4.0 23.8 - - + +
651B VAL* 4.5 13.7 - - + -
654B ALA* 5.7 0.4 - - + -
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Residues in contact with ILE 630 (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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496B LEU* 5.7 2.9 - - + -
583B CYS* 4.1 15.4 - - + +
586B MET* 3.8 31.0 - - + -
587B LEU* 4.4 12.1 - - + -
590B LEU* 4.0 13.2 - - + -
618B ILE* 3.8 32.8 - - + -
626B THR* 3.1 30.4 + - + +
627B ALA 3.6 5.6 - - - +
629B ALA* 1.3 75.3 - - + +
631B GLN* 1.3 64.0 + - - +
633B GLY* 3.3 2.1 + - - -
634B LEU* 3.1 42.8 + - + +
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Residues in contact with GLN 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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615B VAL* 3.7 42.6 - - + +
618B ILE* 3.9 6.2 - - + +
627B ALA* 2.9 20.8 + - - +
628B GLN* 3.5 20.7 - - + +
630B ILE* 1.3 74.9 - - - +
632B GLU* 1.3 60.8 + - + +
634B LEU* 3.1 16.8 + - - +
635B ARG* 3.4 14.3 + - - +
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Residues in contact with GLU 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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628B GLN* 2.9 46.2 + - + +
629B ALA* 3.7 4.3 - - - +
631B GLN* 1.3 77.6 - - + +
633B GLY* 1.3 60.3 + - - +
634B LEU 3.2 0.2 - - - -
635B ARG* 3.3 47.5 + - - +
641B ARG* 3.7 1.4 - - - +
642B VAL* 3.5 30.9 + - + +
647B LEU* 5.2 0.4 - - + -
650B LYS* 2.9 39.7 + - - +
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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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579B VAL* 3.9 15.0 - - - -
580B TRP* 3.5 17.5 + - - -
583B CYS* 3.7 20.4 - - - -
629B ALA 2.9 10.7 + - - -
630B ILE 3.3 1.3 + - - -
632B GLU* 1.3 76.6 - - - +
634B LEU* 1.3 59.6 + - - +
635B ARG 3.6 0.9 - - - -
641B ARG* 3.2 20.9 - - - -
642B VAL* 3.8 5.5 - - - +
647B LEU* 4.6 1.1 - - - -
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Residues in contact with LEU 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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580B TRP* 3.2 50.8 - - + +
583B CYS* 3.6 23.1 - - + -
584B CYS* 4.3 8.3 - - - +
587B LEU* 4.0 20.4 - - + -
613B PRO* 3.3 22.4 - - + +
614B PRO* 4.2 7.2 - - + -
615B VAL* 4.2 23.0 - - + +
630B ILE* 3.1 33.1 + - + +
631B GLN 3.1 8.4 + - - +
633B GLY* 1.3 78.0 - - - +
635B ARG* 1.3 61.9 + - - +
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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