Contacts of the strand formed by residues 99 - 106 (chain A) in PDB entry 3ZWG
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 THR 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A MET* 3.5 15.6 - - + +
91A ALA* 4.4 4.7 - - + -
92A TYR 3.5 2.5 - - - -
94A MET* 4.8 1.6 - - - -
98A ASN* 1.3 78.6 + - - +
100A LEU* 1.3 74.2 + - - +
101A ALA* 3.8 6.0 + - + +
121A VAL* 3.4 9.1 - - - +
122A TYR* 2.8 46.0 + - + -
124A GLY 2.8 18.8 + - - -
125A GLN* 3.3 4.2 - - - -
126A LYS* 2.9 36.8 + - + +
132A MET* 4.9 1.3 - - + -
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Residues in contact with LEU 100 (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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37A ILE* 4.8 3.6 - - + -
45A TRP* 3.5 42.2 - - + -
90A ILE* 3.6 0.9 - - - +
91A ALA* 3.4 4.0 - - - -
92A TYR* 2.9 44.4 + - + +
94A MET* 4.1 20.1 - - + +
98A ASN 4.3 0.2 - - - -
99A THR* 1.3 72.8 - - - +
101A ALA* 1.3 63.3 + - - +
102A VAL* 4.3 16.8 - - + +
119A VAL* 4.1 12.1 - - + -
120A ARG 3.9 0.7 - - - +
121A VAL* 3.9 22.2 - - + +
154A LEU* 4.1 15.3 - - + -
176A VAL* 4.1 12.1 - - + -
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Residues in contact with ALA 101 (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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89A VAL* 4.4 0.2 - - + -
90A ILE 3.2 6.7 - - - +
91A ALA* 5.1 0.2 - - - -
99A THR* 3.8 2.7 + - + -
100A LEU* 1.3 74.9 - - - +
102A VAL* 1.3 66.7 + - - +
118A ASN 3.9 0.7 - - - +
119A VAL* 3.5 2.4 - - - +
120A ARG* 3.0 36.9 + - + +
122A TYR* 3.9 16.6 - - + -
132A MET* 3.7 31.0 - - + -
136A LEU* 4.1 9.1 - - + +
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Residues in contact with VAL 102 (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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35A VAL* 5.3 0.7 - - + -
37A ILE* 4.1 24.5 - - + -
88A GLY 3.8 0.2 - - - +
89A VAL* 3.0 6.3 - - - -
90A ILE* 2.7 56.1 + - + +
100A LEU* 4.6 12.6 - - + -
101A ALA* 1.3 79.4 - - - +
103A LEU* 1.3 70.9 + - - +
104A PHE* 4.1 2.0 + - + -
118A ASN 3.3 10.5 - - - +
119A VAL* 4.3 16.4 - - + -
136A LEU* 4.6 0.2 - - - -
172A LEU* 4.4 6.5 - - + -
174A ILE* 3.5 25.6 - - + -
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Residues in contact with LEU 103 (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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88A GLY 3.3 13.5 - - - +
89A VAL* 4.3 3.1 - - + -
101A ALA 4.3 0.2 - - - -
102A VAL* 1.3 78.2 - - - +
104A PHE* 1.3 83.3 + - - +
105A SER* 4.2 1.6 - - - +
116A TRP 5.1 1.3 - - - +
117A TRP* 3.2 13.6 - - - +
118A ASN* 2.9 55.7 + - + +
133A TYR* 4.2 25.8 - - + -
136A LEU* 3.6 37.0 - - + +
137A TYR* 3.9 17.0 - - + +
142A PRO* 4.2 5.8 - - + -
172A LEU* 4.4 0.2 - - - +
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Residues in contact with PHE 104 (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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33A ILE* 3.8 39.5 - - + -
35A VAL* 4.8 6.3 - - + -
50A THR* 4.5 2.7 - - + -
52A PHE* 3.9 20.4 - + - -
73A TYR* 5.2 4.0 - + - -
74A ASN 6.4 0.4 - - - -
75A GLY* 6.0 0.7 - - - -
86A VAL* 3.9 32.3 - - + -
87A VAL* 3.2 0.9 - - - -
88A GLY* 2.7 71.3 + - - +
89A VAL 4.0 1.8 - - - -
90A ILE* 4.0 31.0 - - + -
102A VAL* 4.4 4.3 - - + -
103A LEU* 1.3 80.6 - - - +
105A SER* 1.3 61.1 + - - +
116A TRP 3.5 7.0 - - - +
117A TRP* 4.4 0.2 - - - +
164A MET* 4.8 0.9 - - + -
172A LEU* 4.2 10.5 - - + -
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Residues in contact with SER 105 (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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87A VAL* 3.2 24.1 - - - +
103A LEU* 4.6 1.3 - - - -
104A PHE* 1.3 74.6 - - - +
106A VAL* 1.3 62.9 + - - +
107A PRO* 3.5 10.3 - - - +
115A ASN* 3.5 7.6 - - - +
116A TRP* 2.7 39.6 + - - +
137A TYR* 3.5 35.9 + - - -
164A MET* 4.1 0.7 - - - +
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Residues in contact with VAL 106 (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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31A ARG* 4.2 7.1 - - + -
32A LYS 4.8 0.4 - - - +
33A ILE* 4.0 12.3 - - + -
85A GLY* 3.0 6.9 - - - -
86A VAL* 2.8 56.0 + - + +
87A VAL* 3.9 3.0 - - - +
105A SER* 1.3 75.5 + - - +
107A PRO* 1.3 61.1 - - - +
110A TYR* 3.6 10.5 - - - +
115A ASN* 3.4 12.1 - - - +
164A MET* 3.8 10.8 - - + -
167A SER 4.3 1.6 - - - +
168A GLY* 3.9 24.7 - - - +
170A ALA* 3.8 23.8 - - + -
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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