Contacts of the helix formed by residues 694 - 704 (chain B) in PDB entry 3T1N
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 THR 694 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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653B THR* 2.9 23.7 + - - +
654B SER* 3.8 21.5 - - - +
692B LEU* 3.0 14.2 + - + +
693B ARG* 1.3 75.6 - - - +
695B LEU* 1.3 65.8 + - - +
696B ASN 3.4 7.8 + - - -
697B VAL* 3.6 10.3 + - - +
698B LEU* 2.9 27.8 + - - +
821D SEP 3.8 30.7 + - - +
822D ASP 3.6 13.2 - - - +
823D GLU* 4.8 0.7 - - - -
824D PHE* 4.7 2.2 - - - -
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Residues in contact with LEU 695 (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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678B ASP* 3.7 15.9 - - - +
694B THR* 1.3 77.0 - - - +
696B ASN* 1.3 99.4 + - - +
698B LEU* 3.4 6.9 + - - +
699B LEU* 3.1 44.7 + - + +
770B PRO* 6.2 3.4 - - + -
774B LYS* 5.0 15.7 - - + +
821D SEP 4.1 22.0 - - - +
822D ASP 4.3 6.0 + - - +
824D PHE* 4.4 15.6 - - + -
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Residues in contact with ASN 696 (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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651B VAL* 4.0 7.1 - - + +
652B MET 3.9 11.5 + - - -
653B THR* 4.1 15.7 - - + +
677B PRO 3.7 9.7 + - - -
678B ASP* 3.3 17.6 + - - +
679B VAL* 3.1 42.9 + - + +
686B VAL* 4.9 5.0 - - + +
694B THR* 3.2 1.4 + - - +
695B LEU* 1.3 96.1 - - - +
697B VAL* 1.3 65.7 + - - +
699B LEU* 3.2 3.1 + - - +
700B GLY* 2.9 20.4 + - - -
821D SEP 3.2 20.6 + - - -
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Residues in contact with VAL 697 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653B THR* 3.7 25.6 - - + -
686B VAL* 4.9 6.9 - - + +
688B SER* 4.6 6.7 - - - +
692B LEU 3.3 22.9 - - - +
693B ARG* 4.7 3.1 - - + -
694B THR* 3.5 9.5 + - - +
695B LEU 3.5 0.6 - - - -
696B ASN* 1.3 75.5 - - - +
698B LEU* 1.3 63.1 + - - +
700B GLY* 3.2 2.0 + - - -
701B ILE* 3.1 31.0 + - + +
707B VAL* 4.6 13.4 - - + +
734B PHE* 3.5 42.0 - - + -
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Residues in contact with LEU 698 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693B ARG* 3.2 43.1 - - + +
694B THR 2.9 27.6 + - - +
695B LEU* 3.4 9.2 - - - +
696B ASN 3.2 0.4 - - - -
697B VAL* 1.3 79.3 - - - +
699B LEU* 1.3 62.1 + - - +
701B ILE* 3.0 21.3 + - + +
702B ALA* 3.2 12.0 + - - +
778B LEU* 4.1 17.8 - - + +
817B LEU* 4.4 26.2 - - + +
820B ILE* 4.4 20.9 - - + +
821B THR* 4.1 10.5 - - - +
824D PHE* 5.0 6.3 - - + -
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Residues in contact with LEU 699 (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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678B ASP* 5.8 0.9 - - + -
679B VAL* 4.0 25.1 - - + +
695B LEU* 3.1 38.5 + - + +
696B ASN* 3.7 8.7 - - - +
698B LEU* 1.3 79.6 - - - +
700B GLY* 1.3 59.8 + - - +
702B ALA* 3.8 4.3 + - - +
703B ARG* 3.4 30.0 + - - +
774B LYS* 4.5 21.5 - - + +
777B GLU* 3.8 37.5 - - + +
778B LEU* 3.6 26.0 - - + -
781B LEU* 4.4 3.7 - - + +
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Residues in contact with GLY 700 (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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679B VAL* 4.7 2.2 - - - -
686B VAL* 4.5 9.6 - - - -
696B ASN 2.9 13.1 + - - -
697B VAL* 3.2 4.7 + - - -
698B LEU 3.0 0.4 - - - -
699B LEU* 1.3 77.4 - - - +
701B ILE* 1.3 58.9 + - - +
703B ARG 3.4 0.5 + - - -
704B GLY 2.9 22.2 + - - -
705B CYS* 3.0 32.4 + - - +
707B VAL* 4.8 5.6 - - - -
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Residues in contact with ILE 701 (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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693B ARG* 6.1 0.4 - - + -
697B VAL* 3.1 31.1 + - + +
698B LEU* 3.0 14.3 + - + +
700B GLY* 1.3 76.3 - - - +
702B ALA* 1.3 65.8 + - - +
704B GLY* 3.2 10.0 + - - +
707B VAL* 4.9 4.3 - - + -
734B PHE* 4.4 18.6 - - + -
736B ALA* 3.8 26.9 - - + -
737B ALA* 4.5 18.2 - - + +
740B CYS* 3.2 27.5 - - - +
820B ILE* 4.0 15.9 - - + +
821B THR* 4.6 19.7 - - + +
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Residues in contact with ALA 702 (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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698B LEU 3.2 8.4 + - - +
699B LEU 4.0 5.6 - - - +
700B GLY 3.3 0.2 - - - -
701B ILE* 1.3 80.5 - - - +
703B ARG* 1.3 59.9 + - - +
740B CYS* 5.3 1.3 - - - -
751B TYR* 3.5 16.5 + - - -
752B ARG* 5.8 0.2 - - - -
753B GLY* 4.7 1.6 + - - -
778B LEU* 4.6 9.9 - - + +
781B LEU* 3.7 45.6 - - + +
782B CYS* 3.9 22.6 - - - -
820B ILE* 4.8 2.2 - - + +
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Residues in contact with ARG 703 (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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679B VAL* 3.6 22.0 - - - +
680B CYS* 3.6 17.5 + - - +
681B GLU* 3.2 48.1 + - - +
683B THR 5.2 1.8 - - - +
699B LEU* 3.4 17.9 + - - +
700B GLY 3.4 1.0 + - - +
701B ILE 3.1 0.6 - - - -
702B ALA* 1.3 76.7 - - - +
704B GLY* 1.3 62.3 + - - +
705B CYS* 3.4 17.2 - - - -
744B CYS* 3.7 7.6 - - - -
751B TYR* 3.4 21.2 - - - -
777B GLU* 3.3 23.8 + - - -
781B LEU* 3.8 33.0 - - + +
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Residues in contact with GLY 704 (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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700B GLY 2.9 5.3 + - - -
701B ILE* 3.2 4.9 + - - -
703B ARG* 1.3 79.2 - - - +
705B CYS* 1.3 65.8 + - - +
737B ALA 5.3 0.4 - - - -
740B CYS* 3.7 17.0 - - - -
741B ARG* 3.1 39.7 - - - +
744B CYS* 4.4 1.7 - - - +
745B HIS* 3.5 12.5 + - - -
751B TYR* 4.3 1.1 - - - -
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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