Contacts of the strand formed by residues 121 - 125 (chain A) in PDB entry 3U7U
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 GLY 121 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ARG 2.8 15.7 + - - -
90A TYR* 3.4 6.6 - - - -
91A ALA* 2.7 29.6 + - - +
92A LEU 3.2 6.8 + - - -
117A ILE* 5.1 0.2 - - - -
120A GLY* 1.3 73.4 - - - -
122A VAL* 1.4 65.3 + - - +
142A VAL* 5.2 0.4 - - - -
148A SER* 4.3 9.9 - - - -
150A LEU* 3.4 15.0 - - - -
151A THR* 4.3 3.1 - - - -
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Residues in contact with VAL 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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90A TYR* 4.2 2.4 - - - -
92A LEU* 3.4 11.9 - - + +
117A ILE* 3.8 21.5 - - + -
121A GLY* 1.4 75.3 - - - +
123A TYR* 1.3 62.4 + - - +
124A VAL* 3.7 24.5 - - + +
138A TRP* 3.8 46.7 - - + +
142A VAL* 4.0 15.7 - - + -
150A LEU 3.2 16.5 + - - +
151A THR* 4.2 6.8 + - - -
152A LEU 3.6 18.9 + - - +
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Residues in contact with TYR 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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86A TYR* 6.0 0.4 - + - -
90A TYR* 3.6 48.6 - + + -
92A LEU 2.7 10.6 + - - +
93A ALA* 3.2 4.1 - - + -
94A ILE 2.7 32.2 + - - +
95A PHE* 3.5 48.8 - + + +
122A VAL* 1.3 71.7 - - - +
124A VAL* 1.3 54.3 + - - +
125A ASP* 3.2 35.2 + - + +
126A GLN* 4.5 5.7 - - - +
152A LEU 4.4 2.9 - - - -
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Residues in contact with VAL 124 (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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92A LEU* 4.8 1.3 - - + -
94A ILE* 3.2 30.3 - - + +
109A LEU* 5.0 1.1 - - + -
122A VAL* 3.7 21.1 - - + -
123A TYR* 1.3 76.1 - - - +
125A ASP* 1.3 60.1 + - - +
127A ASN* 3.7 16.4 - - - +
130A LEU* 4.0 19.7 - - + -
133A ALA* 4.7 4.7 - - + -
138A TRP* 4.2 12.6 - - + -
152A LEU 3.4 9.3 + - - +
153A VAL* 3.3 25.8 - - + -
154A SER 3.1 21.9 + - - -
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Residues in contact with ASP 125 (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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94A ILE 3.0 5.3 + - - -
95A PHE* 3.0 24.2 - - - +
123A TYR* 3.2 39.2 + - + -
124A VAL* 1.3 76.3 - - - +
126A GLN* 1.4 99.5 + - - +
127A ASN* 3.2 6.5 - - - +
154A SER* 3.1 33.7 + - - +
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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