Contacts of the strand formed by residues 664 - 671 (chain C) in PDB entry 2W4T
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 HIS 664 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166C ASP* 5.9 4.8 - - + +
168C GLU* 3.0 42.4 - - + +
169C ASN 3.6 3.4 + - - -
170C GLN* 2.7 36.3 - - - +
171C SER 3.6 2.8 + - - -
663C THR* 1.3 74.4 - - - +
665C PRO* 1.3 65.7 - - - +
666C HIS* 3.0 12.0 + - - -
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Residues in contact with PRO 665 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C PHE* 3.7 17.4 - - + -
171C SER* 3.3 11.2 - - - +
173C LEU* 6.1 5.4 - - + +
487C PHE* 4.4 18.6 - - + -
491C HIS* 3.0 42.9 + - + +
663C THR* 2.6 29.4 - - - +
664C HIS* 1.3 89.2 - - - +
666C HIS* 1.3 62.0 - - - +
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Residues in contact with HIS 666 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C LEU 5.5 3.4 - - - +
119C PHE* 3.6 3.4 - - - -
145C LYS* 5.8 5.2 - - - +
155C VAL* 4.0 25.5 + - + +
156C ALA* 5.4 1.3 - - - -
159C ALA* 2.7 36.8 - - + +
170C GLN* 3.4 7.6 - - - +
171C SER 2.2 52.7 + - - -
172C CYS* 3.1 35.6 - - + +
173C LEU 3.2 3.2 + - - -
456C ILE* 3.6 10.5 - - + -
664C HIS 3.0 14.4 - - - -
665C PRO* 1.3 74.1 - - - +
667C PHE* 1.3 61.4 + - - +
668C VAL* 4.9 0.3 - - - +
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Residues in contact with PHE 667 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C PHE* 2.4 60.7 - + + +
120C CYS* 2.9 29.5 + - - -
155C VAL* 5.3 0.7 - - - +
173C LEU* 3.0 22.7 - - + +
175C THR* 2.0 52.5 - - + -
484C LEU* 4.9 4.5 - - + -
488C PHE* 4.1 27.6 - + + -
666C HIS* 1.3 74.3 - - - +
668C VAL* 1.3 75.4 + - - +
669C ARG* 3.1 28.9 - - + -
694C ASN* 6.4 0.7 - - + -
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Residues in contact with VAL 668 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C CYS* 2.9 26.9 - - - -
122C ALA* 6.1 3.1 - - + -
152C LEU* 4.0 15.7 - - + -
155C VAL* 4.5 11.7 - - + -
172C CYS* 5.0 5.2 - - + -
173C LEU 3.0 2.2 + - - +
174C ILE* 2.3 64.8 - - + +
175C THR 2.8 30.7 + - - +
185C ASN* 5.7 4.7 - - + +
189C VAL* 6.0 3.6 - - + -
666C HIS 4.9 2.7 - - - +
667C PHE* 1.3 82.4 - - - +
669C ARG* 1.3 55.8 + - - +
670C CYS 4.0 0.9 - - - +
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Residues in contact with ARG 669 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C LEU* 4.0 6.3 - - - +
116C SER* 5.2 2.6 + - - -
120C CYS* 2.8 15.6 + - - +
121C ILE* 2.7 48.2 - - - +
122C ALA* 2.8 32.0 + - - +
175C THR* 3.5 4.3 - - - +
667C PHE* 3.1 22.4 - - + -
668C VAL* 1.3 70.3 - - - +
670C CYS* 1.3 58.2 + - - +
671C ILE* 2.9 34.5 - - - +
690C GLN* 3.3 25.5 + - - +
691C LEU* 4.0 17.7 - - - +
694C ASN* 2.8 30.3 - - + -
696C VAL* 3.3 17.2 - - - +
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Residues in contact with CYS 670 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C ALA* 3.3 9.0 - - - -
174C ILE* 5.3 0.9 - - + -
175C THR 2.5 13.9 + - - +
176C GLY* 2.3 50.1 - - - -
177C GLU* 2.9 12.9 - - - +
180C ALA* 2.5 37.0 - - + +
181C GLY* 3.9 12.1 - - - +
182C LYS* 4.0 13.5 - - + +
185C ASN* 4.9 4.0 - - - +
668C VAL 4.0 0.4 - - - -
669C ARG* 1.3 70.2 - - - +
671C ILE* 1.3 66.8 + - - +
690C GLN* 3.6 10.0 + - - -
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Residues in contact with ILE 671 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C LEU* 5.2 3.1 - - + -
107C TYR* 6.2 0.2 - - + -
122C ALA 3.0 13.3 + - - +
123C VAL* 3.1 40.2 - - + -
124C ASN* 2.9 18.9 + - - +
177C GLU* 3.5 5.2 - - - +
180C ALA* 3.7 4.2 + - - +
669C ARG* 2.9 37.7 - - - +
670C CYS* 1.3 82.1 - - - +
672C ILE* 1.3 63.5 + - - +
673C PRO* 3.7 19.7 - - + -
687C VAL* 4.7 15.3 - - + -
690C GLN* 4.5 9.0 - - + +
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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