Contacts of the strand formed by residues 128 - 134 (chain H) in PDB entry 4KYI
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 VAL 128 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95H GLN 3.2 17.6 + - - +
96H ALA* 3.5 3.7 - - - +
97H ALA 2.8 30.8 + - - +
126H ASN* 4.3 7.2 - - - +
127H ILE* 1.3 76.8 - - - +
129H ILE* 1.3 65.8 + - - +
159H LEU* 5.0 6.3 - - + -
178H ILE* 4.0 25.9 - - + +
181H LYS* 3.5 40.8 - - + +
182H LEU* 3.7 11.7 - - + -
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Residues in contact with ILE 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H ALA* 3.6 4.0 - - + +
99H VAL* 4.0 25.6 - - + -
116H VAL* 4.4 9.0 - - + +
119H LEU* 3.7 39.9 - - + +
120H GLN* 3.9 25.8 - - - +
127H ILE* 3.6 27.7 + - + +
128H VAL* 1.3 75.2 - - - +
130H ALA* 1.3 62.6 + - - +
157H SER 5.0 0.3 - - - +
158H LEU* 3.6 27.0 - - + +
159H LEU* 3.4 19.9 + - - +
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Residues in contact with ALA 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H ALA 2.9 15.2 + - - +
98H ILE* 3.2 6.3 - - + +
99H VAL 2.7 31.2 + - - -
128H VAL* 5.5 0.9 - - + -
129H ILE* 1.3 77.4 - - - +
131H LEU* 1.3 56.3 + - - +
159H LEU* 3.2 26.0 - - + +
174H ILE* 4.6 10.8 - - + -
178H ILE* 3.9 25.8 - - + -
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Residues in contact with LEU 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H VAL* 3.3 36.3 - - + +
101H TYR* 4.0 32.1 - - + -
109H PHE* 4.7 7.4 - - + -
112H ALA* 4.1 8.5 - - + -
116H VAL* 4.5 7.2 - - + -
129H ILE 4.3 0.4 - - - -
130H ALA* 1.3 73.5 - - - +
132H ALA* 1.3 61.3 + - - +
149H ALA 4.7 4.5 - - - +
152H TYR* 3.9 30.7 - - + -
153H ALA* 5.3 1.3 - - + -
158H LEU* 4.4 14.8 - - + +
159H LEU 2.8 10.1 + - - +
160H PHE* 3.4 19.8 - - + -
161H MET 3.4 22.5 + - - -
174H ILE* 3.9 4.0 - - - +
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Residues in contact with ALA 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H LEU* 4.9 3.6 - - + -
98H ILE* 4.1 12.3 - - + -
99H VAL 2.7 14.1 + - - +
100H VAL* 3.5 10.8 - - + +
101H TYR* 2.9 31.5 + - - -
131H LEU* 1.3 76.8 - - - +
133H GLY* 1.3 59.7 + - - +
134H ASN 3.2 3.3 + - - -
161H MET 3.4 4.0 - - - -
163H THR* 4.2 15.5 - - + +
174H ILE* 3.9 18.6 - - + -
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Residues in contact with GLY 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101H TYR* 3.5 33.5 - - - -
103H ILE* 3.8 7.8 - - - +
132H ALA* 1.3 67.2 - - - +
134H ASN* 1.3 63.9 + - - +
136H ALA* 4.1 1.4 - - - +
160H PHE* 4.0 1.4 - - - -
161H MET 3.0 13.6 + - - -
162H GLU* 3.4 11.1 - - - +
163H THR 2.8 24.4 + - - +
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Residues in contact with ASN 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H VAL 2.6 28.7 + - - +
33H GLY* 3.5 11.3 + - - -
37H LEU* 3.4 18.1 - - - +
100H VAL* 3.7 16.2 - - + -
101H TYR 2.8 10.7 + - - +
102H ASP* 4.8 0.2 - - - -
103H ILE* 3.3 19.9 + - - +
132H ALA 3.2 3.2 + - - -
133H GLY* 1.3 74.5 - - - -
135H LYS* 1.3 79.8 + - - +
136H ALA 3.3 0.2 - - - -
163H THR* 2.8 24.7 + - - +
165H ALA 3.5 9.7 + - - -
301H GNP 3.2 24.4 + - - -
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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