Contacts of the strand formed by residues 94 - 102 (chain A) in PDB entry 3FL7
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 ILE 94 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 3.9 28.9 - - + -
91A ALA* 4.3 7.4 - - + -
92A GLU 4.1 0.4 - - - -
93A ARG* 1.3 75.3 - - - +
95A PHE* 1.3 63.4 + - - +
96A ILE* 4.0 12.8 - - + -
123A TYR* 6.0 0.7 - - + -
169A SER* 3.1 22.7 - - - -
170A VAL* 2.9 46.8 + - + +
173A LEU* 3.6 25.6 - - + -
178A PHE* 3.7 33.0 - - + -
180A LEU* 4.6 1.8 - - + -
196A VAL* 3.7 13.9 - - + -
197A TYR 3.8 4.5 - - - +
198A TYR* 4.9 0.2 - - + -
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Residues in contact with PHE 95 (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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93A ARG* 3.8 36.3 - - + -
94A ILE* 1.3 75.6 - - - +
96A ILE* 1.3 61.2 + - - +
97A GLU 4.1 0.4 - - - -
167A GLU* 3.8 20.2 - - - -
168A ARG 3.6 3.1 - - - -
169A SER* 3.8 18.8 - - - -
195A ARG 3.4 1.6 - - - +
196A VAL* 3.1 25.6 - - - +
197A TYR* 2.9 54.1 + + + +
198A TYR* 4.5 0.7 - - - -
199A LYS* 3.6 40.4 - - + -
249A VAL* 4.4 11.4 - - + -
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Residues in contact with ILE 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ILE* 4.0 12.6 - - + -
95A PHE* 1.3 76.4 - - - +
97A GLU* 1.3 58.4 + - - +
98A LEU* 3.9 22.7 + - + +
121A LEU* 4.4 16.2 - - + -
142A ILE* 3.8 21.5 - - + -
166A GLU 3.6 1.9 - - - +
167A GLU* 3.3 6.4 - - - -
168A ARG* 2.8 41.2 + - + +
169A SER* 5.0 0.9 - - - -
170A VAL* 3.9 19.7 - - + -
180A LEU* 3.7 44.4 - - + -
194A VAL* 4.8 0.9 - - + -
195A ARG 3.5 3.6 - - - +
196A VAL* 4.3 4.7 - - + -
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Residues in contact with GLU 97 (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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96A ILE* 1.3 73.1 - - - +
98A LEU* 1.3 63.5 + - - +
99A LYS* 2.9 30.0 + - - +
165A VAL* 4.3 19.2 - - + +
166A GLU 3.6 4.7 - - - +
167A GLU* 4.0 21.2 - - + +
193A SER* 3.8 2.6 + - - +
194A VAL* 3.3 5.4 + - - -
195A ARG* 2.7 80.2 + - + +
197A TYR* 4.7 3.4 - - + -
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Residues in contact with LEU 98 (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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96A ILE* 3.9 21.3 - - + +
97A GLU* 1.3 80.2 - - - +
99A LYS* 1.3 65.1 + - - +
100A PHE* 4.3 12.2 - - + -
119A PHE* 4.2 21.1 - - + -
121A LEU* 4.8 7.2 - - + -
145A ILE* 4.3 23.6 - - + -
164A ASN 3.9 0.3 - - - +
165A VAL* 3.5 6.9 - - - +
166A GLU* 3.0 37.1 + - + +
168A ARG* 6.4 0.4 - - + -
182A PHE* 3.7 33.2 - - + -
191A LEU* 4.5 4.3 - - + -
193A SER 3.3 3.8 - - - +
194A VAL* 4.0 16.2 - - + -
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Residues in contact with LYS 99 (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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97A GLU* 2.9 30.2 + - - +
98A LEU* 1.3 78.5 - - - +
100A PHE* 1.3 64.9 + - - +
163A LEU* 4.3 27.1 - - + -
164A ASN 3.4 5.8 - - - +
165A VAL* 4.2 25.1 - - + -
191A LEU* 3.6 2.6 - - - +
192A LEU* 2.9 27.6 + - + -
193A SER* 3.0 35.1 + - - +
195A ARG* 5.0 4.2 - - - +
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Residues in contact with PHE 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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98A LEU* 4.3 8.7 - - + -
99A LYS* 1.3 80.8 - - - +
101A THR* 1.3 64.5 + - - +
102A VAL* 3.7 31.2 - - + -
119A PHE* 3.8 20.2 - + + -
145A ILE* 3.5 29.8 - - + -
146A ALA 3.8 13.0 - - - -
147A PRO* 3.9 7.9 - - + -
163A LEU* 3.8 7.7 - - - +
164A ASN* 3.0 63.8 + - + -
166A GLU* 3.7 18.6 - - + -
189A VAL* 4.4 3.6 - - + -
190A ALA 3.2 16.4 - - - +
191A LEU* 4.3 7.9 - - + -
192A LEU* 4.5 1.3 - - - -
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Residues in contact with THR 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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100A PHE* 1.3 79.0 - - - +
102A VAL* 1.3 62.7 + - - +
151A THR* 4.6 15.6 + - + -
161A VAL* 5.7 4.5 - - + -
162A LYS 3.9 17.7 - - - +
163A LEU* 3.8 18.6 - - + -
164A ASN* 4.1 3.6 - - - +
188A CYS 4.6 0.9 + - - -
189A VAL* 3.4 10.4 - - - +
190A ALA* 3.1 41.6 + - + +
192A LEU* 4.7 8.1 - - + -
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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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100A PHE* 3.7 19.7 - - + -
101A THR* 1.3 79.2 - - - +
103A ARG* 1.3 73.1 + - - +
116A LYS 5.1 1.1 - - - +
117A GLU* 3.3 37.2 - - + +
119A PHE* 5.0 4.5 - - + -
145A ILE 6.0 0.2 - - - +
147A PRO* 3.7 26.9 - - + -
149A GLU 5.0 0.6 + - - -
150A ILE* 3.6 7.6 - - + +
151A THR* 3.1 26.8 + - - +
164A ASN* 4.2 4.9 - - - +
187A ALA* 5.1 3.1 - - + -
188A CYS 3.6 9.6 - - - +
189A VAL* 4.4 11.7 - - + -
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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