Contacts of the strand formed by residues 96 - 104 (chain L) in PDB entry 4G7Z
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 96 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89L PHE* 4.1 2.1 - - - -
94L LEU* 3.0 20.5 - - + +
95L GLN* 1.3 86.4 - - + +
97L VAL* 1.3 72.9 + - - +
143L ARG* 3.4 22.8 + - - +
144L VAL 3.2 10.2 + - - -
145L ASP* 2.9 26.7 + - - +
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Residues in contact with VAL 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89L PHE* 3.6 18.2 - - + -
94L LEU* 3.6 27.6 - - + -
96L THR* 1.3 87.9 + - - +
98L THR* 1.3 69.5 + - - +
99L LEU* 3.5 25.6 - - + -
117L VAL* 3.7 24.0 - - + -
118L ALA* 6.0 0.4 - - + -
120L VAL* 4.4 6.3 - - + -
142L VAL 3.8 0.3 - - - +
143L ARG* 3.4 5.2 - - - +
144L VAL* 2.7 37.6 + - + +
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Residues in contact with THR 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97L VAL* 1.3 83.3 + - - +
99L LEU* 1.3 67.5 + - - +
100L LEU* 4.1 14.0 - - + +
117L VAL* 4.3 8.7 - - - +
141L GLU* 3.9 34.5 - - + +
142L VAL 3.5 10.1 - - - +
143L ARG* 4.9 5.4 - - + +
160L ASP* 4.1 16.7 + - - +
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Residues in contact with LEU 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85L LEU* 4.8 8.3 - - + -
87L VAL* 4.9 9.9 - - + -
89L PHE* 6.2 0.2 - - + -
97L VAL* 3.5 29.6 - - + -
98L THR* 1.3 73.5 - - - +
100L LEU* 1.3 62.1 - - - +
114L PHE* 3.8 35.0 - - + -
115L LEU 5.0 2.2 - - - +
117L VAL* 5.0 12.8 - - + -
120L VAL* 5.4 10.3 - - + -
122L ILE* 5.2 8.3 - - + -
140L MET 3.8 0.2 - - - +
141L GLU* 3.1 6.2 - - - -
142L VAL* 2.8 56.3 + - + +
144L VAL* 4.1 21.1 - - + -
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Residues in contact with LEU 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98L THR* 4.1 15.9 - - + +
99L LEU* 1.3 77.8 - - - +
101L LEU* 1.3 61.6 + - - +
114L PHE* 3.4 6.2 - - - -
115L LEU* 3.2 55.2 + - + +
117L VAL* 5.6 5.1 - - + +
140L MET 3.5 4.9 - - - +
141L GLU* 3.9 28.7 - - + +
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Residues in contact with LEU 101 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100L LEU* 1.3 76.9 - - - +
102L LYS* 1.3 71.0 + - - +
103L ALA* 4.7 2.2 - - + +
109L VAL* 3.6 29.8 - - + -
110L LYS 4.3 4.0 - - - +
113L ASP* 3.5 34.1 - - + +
114L PHE* 3.6 28.9 - - + +
115L LEU* 5.5 1.8 - - - -
129L ILE* 5.8 3.1 - - + -
138L LEU* 3.8 30.7 - - + -
139L ASN* 3.6 2.8 - - - +
140L MET* 2.9 44.4 + - + +
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Residues in contact with LYS 102 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59L GLU* 5.6 0.7 - - - +
101L LEU* 1.3 78.7 - - - +
103L ALA* 1.3 67.3 + - - +
104L GLU* 4.0 22.4 + - - +
113L ASP 5.3 2.0 + - - +
115L LEU* 6.1 0.6 - - - +
137L ARG* 6.2 0.8 - - - +
138L LEU 3.2 16.6 - - - +
139L ASN* 3.3 28.9 - - + +
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Residues in contact with ALA 103 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101L LEU* 4.7 5.4 - - + +
102L LYS* 1.3 81.4 + - - +
104L GLU* 1.3 68.7 + - - +
107L LYS* 4.3 28.3 - - + +
109L VAL* 4.6 18.6 - - + -
113L ASP* 5.6 2.5 - - + +
132L LEU* 3.6 4.8 - - + +
138L LEU* 3.0 29.3 + - + +
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Residues in contact with GLU 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102L LYS* 4.0 17.8 + - - +
103L ALA* 1.3 80.4 - - - +
105L GLY* 1.3 71.5 + - - +
106L PRO* 4.6 0.2 - - - +
107L LYS* 3.8 15.8 - - - +
132L LEU* 3.7 5.5 - - - +
135L GLY 5.8 0.2 - - - -
136L GLY 3.2 15.5 - - - +
137L ARG* 3.1 41.5 + - + +
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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