Contacts of the strand formed by residues 76 - 85 (chain A) in PDB entry 1F5J
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 SER 76 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TRP* 3.7 14.5 - - - -
70A TYR* 2.6 31.6 + - - -
72A PRO* 3.5 20.2 - - - -
74A GLY 3.1 2.8 + - - -
75A ASN* 1.3 81.4 + - - +
77A TYR* 1.3 70.3 + - - +
97A TRP* 3.1 4.2 - - - +
98A GLY 2.9 21.7 + - - +
100A TRP 4.8 0.5 + - - +
179A VAL* 4.4 0.2 - - - +
180A GLU 2.6 23.9 + - - -
181A GLY* 4.1 0.7 - - - -
182A TYR 4.8 0.2 - - - +
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Residues in contact with TYR 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 3.2 9.9 + - - -
75A ASN* 3.9 18.2 + - - -
76A SER* 1.3 87.7 + - - +
78A LEU* 1.3 59.5 + - - +
79A CYS* 4.0 11.7 - - + -
92A TYR* 3.9 11.7 - + - -
94A VAL* 4.5 6.3 - - + -
96A SER 3.6 6.7 - - - +
97A TRP* 4.4 0.9 - - + -
100A TRP* 3.4 24.1 - + - -
102A PRO* 3.5 39.6 - - + +
103A PRO* 5.2 0.3 - - - +
141A TRP* 3.9 22.2 - + - -
178A CYS 4.3 0.2 - - - -
179A VAL* 3.4 5.2 - - - -
180A GLU* 2.9 68.6 + - + +
182A TYR* 6.0 3.1 - - + +
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TYR* 4.2 9.6 - - + -
68A ALA* 4.1 24.7 - - + -
70A TYR* 3.6 24.8 + - + -
77A TYR* 1.3 72.1 - - - +
79A CYS* 1.3 65.8 + - - +
94A VAL* 3.8 0.5 - - - -
95A GLU* 2.9 27.0 + - + -
96A SER* 2.9 13.7 + - - +
148A ARG 4.1 5.4 - - - +
149A THR* 4.0 37.9 - - + -
177A LEU* 4.4 14.6 - - + -
178A CYS 3.5 9.0 - - - +
179A VAL* 4.0 17.5 - - + -
190A ILE* 4.5 2.9 - - + -
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Residues in contact with CYS 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A TYR* 4.4 9.6 - - + -
78A LEU* 1.3 80.1 - - - +
80A ILE* 1.3 70.6 + - - +
81A TYR* 4.0 9.9 - - - -
92A TYR* 3.6 29.2 - - + -
93A ILE 3.2 14.6 - - - +
94A VAL* 3.8 15.3 - - + -
95A GLU* 4.3 3.8 - - - +
177A LEU* 3.5 6.5 - - - +
178A CYS* 2.6 56.0 + - - -
180A GLU* 5.3 0.7 - - - -
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Residues in contact with ILE 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ILE* 4.0 26.2 - - + -
66A TYR* 5.2 3.1 - - + -
79A CYS* 1.3 74.9 - - - +
81A TYR* 1.3 63.5 + - - +
91A PHE* 5.2 4.0 - - + -
92A TYR* 3.4 5.0 - - - -
93A ILE* 2.9 50.2 + - + +
95A GLU* 5.2 2.7 - - + -
153A VAL* 3.9 32.5 - - + -
155A VAL* 4.1 12.3 - - + -
175A ILE* 3.8 24.2 - - + -
176A THR 3.1 11.2 - - - +
177A LEU* 3.9 23.1 - - + -
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Residues in contact with TYR 81 (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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45A LEU* 3.6 22.5 - - + +
47A ARG* 3.5 41.7 + - - -
79A CYS* 4.0 4.0 - - - -
80A ILE* 1.3 76.5 - - - +
82A GLY* 1.3 57.8 + - - +
83A TRP* 2.8 33.2 + + - -
90A GLU* 2.5 40.1 + - + -
91A PHE* 3.4 15.7 - - - -
92A TYR* 3.7 25.8 - + - -
174A GLN* 4.8 0.2 - - - -
175A ILE 3.6 0.2 - - - -
176A THR* 2.7 48.2 + - - +
178A CYS* 3.7 21.8 - - + -
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Residues in contact with GLY 82 (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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81A TYR* 1.3 81.7 - - - +
83A TRP* 1.3 71.6 + - - -
90A GLU* 3.6 2.8 - - - +
91A PHE* 3.0 43.6 + - - +
174A GLN* 3.2 20.2 - - - -
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Residues in contact with TRP 83 (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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47A ARG* 4.5 3.0 - - - +
81A TYR* 2.8 28.5 + + - -
82A GLY* 1.3 77.9 - - - -
84A SER* 1.3 56.5 + - - +
88A LEU* 3.7 28.5 - - + -
89A VAL 3.3 17.9 - - - -
90A GLU* 3.4 30.7 - - + -
91A PHE* 3.5 8.9 - - - -
129A PRO 4.5 1.6 - - - -
130A SER* 3.5 39.0 - - - -
131A ILE* 3.7 40.9 - - + +
137A PHE* 3.6 27.8 - + - -
172A ILE* 3.6 4.2 - - - -
173A ASP* 2.8 34.7 + - + -
174A GLN* 3.3 19.8 + - + +
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Residues in contact with SER 84 (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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83A TRP* 1.3 74.7 - - - +
85A THR* 1.3 69.4 + - - +
87A PRO 3.1 10.6 + - - -
88A LEU* 3.2 8.1 - - - +
89A VAL* 2.8 28.3 + - - +
169A LEU* 3.7 27.2 - - - -
170A GLY 2.8 28.9 + - - -
171A THR 3.1 9.6 + - - -
172A ILE* 4.3 6.5 - - - -
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Residues in contact with THR 85 (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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84A SER* 1.3 78.7 + - - +
86A ASN* 1.3 73.7 + - - +
87A PRO 3.0 5.3 - - - +
88A LEU* 4.0 9.6 - - + +
131A ILE* 3.8 23.8 - - + -
132A VAL* 5.3 6.7 - - + -
171A THR* 2.8 46.8 + - - +
173A ASP* 4.8 7.9 - - + +
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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