Contacts of the strand formed by residues 119 - 123 (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 PHE 119 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A TYR* 3.5 6.6 - - - -
116A SER* 3.0 47.2 + - - +
117A GLY 3.6 2.3 - - - +
118A LEU* 1.3 80.2 - - - +
120A CYS* 1.3 58.9 + - - +
121A ILE* 3.9 3.1 - - + -
488A GLN* 5.1 0.2 - - - -
491A PHE* 3.4 44.2 - + - -
669A PHE* 3.5 26.2 - + + +
671A ARG* 3.8 33.7 - - + -
696A ASN 4.4 0.4 - - - -
697A GLY* 3.2 36.8 - - - -
698A VAL* 3.3 28.7 - - + -
701A GLY* 4.6 4.3 - - - -
702A ILE* 6.0 0.2 - - + -
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Residues in contact with CYS 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A TYR* 4.1 26.0 - - - -
114A THR 5.1 0.7 - - - -
115A TYR* 3.8 26.9 - - + -
118A LEU 3.7 1.5 + - - +
119A PHE* 1.3 72.7 - - - +
121A ILE* 1.3 62.3 + - - +
122A ALA 3.7 0.9 + - - -
145A ARG* 5.5 0.7 - - - +
151A HIS 4.5 1.3 - - - -
152A LEU* 4.3 9.4 - - - -
155A ILE* 4.0 30.3 - - + -
669A PHE 3.1 11.3 + - - +
670A VAL* 3.6 10.8 - - + +
671A ARG 3.1 21.0 + - - -
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Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A MET* 4.7 3.4 - - - -
103A LEU* 3.8 35.4 - - + -
112A ILE 3.4 0.9 - - - +
113A TYR* 3.2 6.0 - - - -
114A THR 2.6 46.7 + - - +
116A SER* 4.1 18.2 - - - -
119A PHE* 4.5 5.6 - - + -
120A CYS* 1.3 75.7 - - - +
122A ALA* 1.3 63.7 + - - +
123A ILE* 4.3 6.5 - - + -
671A ARG* 3.7 11.4 - - + +
673A ILE* 3.5 26.7 - - + -
693A LEU* 4.7 3.6 - - + -
698A VAL* 3.9 35.9 - - + -
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Residues in contact with ALA 122 (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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112A ILE* 3.2 10.1 - - + -
113A TYR* 3.2 34.3 - - + -
120A CYS* 3.7 3.1 + - - +
121A ILE* 1.3 74.7 - - - +
123A ILE* 1.3 63.9 + - - +
124A ASN 3.9 0.3 + - - -
180A ALA 4.8 0.7 - - - +
185A ASN* 4.8 15.6 + - - +
670A VAL* 5.1 6.1 - - + -
671A ARG 3.2 6.4 + - - +
672A CYS* 3.2 9.1 - - - +
673A ILE 3.1 19.6 + - - -
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Residues in contact with ILE 123 (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* 4.2 28.9 - - + +
107A TYR* 3.8 34.1 - - + -
112A ILE* 2.8 36.0 + - - +
121A ILE* 4.3 9.4 - - + -
122A ALA* 1.3 75.2 - - - +
124A ASN* 1.3 66.0 + - - +
125A PRO* 3.3 3.8 - - - +
673A ILE* 3.6 27.1 - - + +
675A PRO* 3.6 30.3 - - + -
684A ILE* 4.6 9.0 - - + -
689A VAL* 5.5 4.5 - - + -
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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