Contacts of the strand formed by residues 666 - 673 (chain A) in PDB entry 3I5G
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 666 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A TYR* 3.6 43.4 - + - +
166A ASP* 4.6 3.9 + - - -
168A GLU* 4.1 19.1 + - - +
169A ASN 3.1 5.8 + - - +
170A GLN* 3.3 32.0 + - - +
171A SER 3.0 20.4 + - - -
494A HIS* 3.6 23.0 + + - -
498A LEU* 5.6 5.0 - - + +
665A THR* 1.3 73.2 - - - +
667A PRO* 1.3 75.1 + - - +
668A HIS* 3.4 17.1 - - - -
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Residues in contact with PRO 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A SER* 3.4 12.8 - - - +
173A LEU* 4.5 2.2 - - + -
490A PHE* 3.4 38.4 - - + -
494A HIS* 3.6 39.5 + - + +
665A THR 3.1 12.6 - - - +
666A HIS* 1.3 92.5 - - - +
668A HIS* 1.3 73.2 + - - +
669A PHE* 3.5 19.5 - - + -
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Residues in contact with HIS 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A ILE* 3.6 27.2 + - + +
158A ASN* 4.8 1.5 - - + +
159A ALA* 3.6 33.6 - - + +
162A TYR* 3.9 13.2 - + - -
170A GLN* 2.6 27.5 + - + -
171A SER 2.9 20.6 + - - +
172A MET* 3.5 6.4 - - + -
173A LEU* 2.9 25.6 + - - +
666A HIS* 3.4 21.2 + - - -
667A PRO* 1.3 81.6 + - - +
669A PHE* 1.3 69.7 + - - +
670A VAL 4.2 0.2 - - - -
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Residues in contact with PHE 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LEU* 4.2 13.7 + - + +
119A PHE* 3.5 25.9 - + + -
120A CYS* 3.1 24.1 + - - +
155A ILE* 4.0 4.4 - - - +
173A LEU* 3.6 21.3 - - + -
487A LEU 5.4 1.1 - - - -
490A PHE* 4.1 9.4 - + - -
491A PHE* 3.5 51.4 - + + -
494A HIS* 4.1 12.3 - + + -
667A PRO* 3.5 43.3 - - + -
668A HIS* 1.3 78.5 - - - +
670A VAL* 1.3 63.3 + - - +
671A ARG* 3.8 20.9 - - - +
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Residues in contact with VAL 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A CYS* 3.6 13.2 - - + +
122A ALA* 5.1 4.5 - - + -
152A LEU* 3.8 28.7 - - + -
155A ILE* 3.3 31.6 - - + -
172A MET* 3.6 20.2 - - + -
173A LEU 3.0 8.0 + - - +
174A ILE* 4.0 25.4 - - + -
175A THR 3.2 16.6 + - - -
185A ASN* 4.7 0.2 - - - +
668A HIS 4.2 0.2 + - - -
669A PHE* 1.3 73.2 - - - +
671A ARG* 1.3 77.7 + - - +
672A CYS* 4.1 11.4 - - - -
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Residues in contact with ARG 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A PHE* 3.8 34.6 - - + -
120A CYS 3.1 10.6 + - - +
121A ILE* 3.7 10.3 - - + -
122A ALA 3.2 21.6 + - - -
173A LEU* 3.0 31.9 + - - +
175A THR* 3.1 34.8 - - - +
488A GLN* 5.2 1.6 + - - -
669A PHE* 3.8 23.2 - - - +
670A VAL* 1.3 87.3 + - - +
672A CYS* 1.3 64.9 + - - +
673A ILE* 3.6 6.8 + - + +
696A ASN* 2.8 61.4 + - - +
698A VAL* 3.9 10.5 - - + -
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Residues in contact with CYS 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ALA* 3.2 9.4 - - - +
174A ILE* 3.8 24.2 - - - -
175A THR 3.2 11.0 + - - +
176A GLY* 3.5 17.7 + - - -
180A ALA* 3.4 26.7 - - + +
182A LYS* 4.0 11.9 - - - -
185A ASN* 3.5 32.5 - - - -
670A VAL* 4.3 5.6 - - - -
671A ARG* 1.3 73.3 - - - +
673A ILE* 1.3 62.1 + - - +
692A GLN* 4.4 2.4 - - - +
696A ASN* 4.9 3.1 + - - +
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Residues in contact with ILE 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LEU* 5.0 2.7 - - + -
121A ILE* 3.5 27.8 - - + -
122A ALA 3.1 7.3 + - - -
123A ILE* 3.6 19.6 - - + +
124A ASN* 3.1 17.0 + - - +
180A ALA* 4.0 4.3 + - - +
671A ARG* 3.7 7.4 - - + +
672A CYS* 1.3 81.6 - - - +
674A ILE* 1.3 68.3 + - - +
675A PRO* 3.1 14.0 - - - +
689A VAL* 4.2 17.9 - - + -
692A GLN* 3.6 22.7 - - + +
693A LEU* 3.5 30.1 - - + -
696A ASN* 4.2 12.6 - - - +
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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