Contacts of the strand formed by residues 116 - 122 (chain A) in PDB entry 3F7F
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 GLN 116 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLU* 3.1 33.1 - - - +
113A VAL* 3.2 20.3 + - + +
114A GLU* 3.0 10.7 + - - +
115A GLN* 1.3 88.4 - - + +
117A LEU* 1.3 63.3 + - - +
118A LEU* 3.7 1.2 - - - +
132A GLN* 3.0 40.4 + - - +
133A LEU 3.4 4.7 - - - +
134A PRO* 3.6 30.0 - - + +
135A LEU* 3.9 5.5 - - - +
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Residues in contact with LEU 117 (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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60A LEU* 4.6 5.8 - - + -
62A LEU* 4.2 22.2 - - + -
68A ILE* 4.6 9.2 - - + -
81A PHE* 3.6 35.0 - - + -
110A ILE* 4.2 15.5 - - + -
111A GLN 3.7 9.9 - - - +
112A GLU* 4.4 5.2 - - + -
116A GLN* 1.3 76.0 - - - +
118A LEU* 1.3 62.3 + - - +
119A VAL* 3.6 5.7 + - + +
131A LEU 3.3 4.9 - - - +
132A GLN* 3.7 0.2 - - - -
133A LEU* 2.7 47.5 + - + +
135A LEU* 4.8 2.4 - - + +
138A LEU* 3.4 32.3 - - + -
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Residues in contact with LEU 118 (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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109A THR* 3.8 1.6 - - - +
110A ILE* 3.4 3.1 - - - -
111A GLN* 2.8 35.5 + - + +
113A VAL* 3.4 38.4 - - + -
116A GLN* 3.6 2.5 + - - +
117A LEU* 1.3 71.6 - - - +
119A VAL* 1.3 58.8 + - - +
120A ASN* 4.1 21.1 + - - +
130A THR* 4.0 14.8 - - + -
131A LEU 3.6 4.5 - - - +
132A GLN* 3.5 35.0 - - + +
168A TYR* 5.2 5.6 - - + -
171A PRO* 4.3 17.5 - - + +
188A LYS* 6.3 0.9 - - + -
194A TYR* 5.0 4.5 - - - +
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Residues in contact with VAL 119 (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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79A LEU* 3.8 19.5 - - + -
81A PHE* 4.2 18.6 - - + -
108A LEU* 4.4 0.9 - - + -
109A THR 3.3 11.0 - - - +
110A ILE* 4.0 20.6 - - + -
117A LEU* 4.1 9.4 - - + +
118A LEU* 1.3 76.5 - - - +
120A ASN* 1.3 63.3 + - - +
121A VAL* 3.8 20.8 - - + +
129A LEU 3.8 0.9 - - - +
130A THR* 3.4 3.5 - - - +
131A LEU* 2.6 62.1 + - + +
133A LEU* 4.7 4.5 - - + -
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Residues in contact with ASN 120 (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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108A LEU* 3.3 1.2 - - - -
109A THR* 2.9 55.8 + - + +
118A LEU* 4.4 16.5 + - - +
119A VAL* 1.3 73.0 - - - +
121A VAL* 1.3 67.4 + - - +
128A PHE* 3.8 32.4 - - + -
129A LEU 3.4 2.2 - - - -
130A THR* 3.3 28.0 - - - +
166A LEU* 4.0 4.0 - - + +
168A TYR* 5.0 10.5 - - - -
171A PRO 6.0 0.2 + - - -
174A SER* 5.5 4.4 + - - -
194A TYR* 3.9 13.1 + - - -
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Residues in contact with VAL 121 (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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72A PHE* 4.7 5.2 - - + -
79A LEU* 5.5 0.9 - - + -
97A LEU* 5.1 6.7 - - + -
101A SER* 3.4 30.5 - - - -
107A THR 3.5 6.3 - - - +
108A LEU* 3.5 29.8 - - + -
119A VAL* 3.8 14.8 - - + +
120A ASN* 1.3 82.5 - - - +
122A ILE* 1.3 60.6 + - - +
123A LEU* 2.9 26.5 + - + +
128A PHE* 4.6 1.7 - - - -
129A LEU* 3.0 39.3 + - + +
131A LEU* 5.7 2.0 - - + -
166A LEU* 4.6 0.6 - - - +
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Residues in contact with ILE 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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101A SER* 3.5 2.1 - - - -
102A MET* 3.0 25.1 + - + -
107A THR* 3.1 21.9 + - + +
121A VAL* 1.3 69.5 - - - +
123A LEU* 1.3 66.0 + - - +
126A GLY 4.8 0.2 - - - -
127A SER 3.2 12.8 - - - +
128A PHE* 3.4 24.4 - - + -
158A PHE* 4.3 18.2 - - + -
163A PRO* 4.2 22.9 - - + -
165A PHE 5.6 0.4 - - - +
166A LEU* 3.9 35.2 - - + +
176A VAL* 4.1 25.6 - - + -
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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