Contacts of the strand formed by residues 119 - 126 (chain A) in PDB entry 4FQP
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 GLY 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A ARG* 4.6 5.2 - - - -
117A ASP 3.7 1.4 + - - -
118A GLU* 1.3 82.7 - - - +
120A ASN* 1.3 63.6 + - - -
121A TYR* 3.3 14.5 - - - -
139A LEU 2.9 26.9 + - - -
1C NAG 3.6 17.0 - - - -
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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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68A ARG* 4.3 1.4 - - - +
69A HIS* 3.1 51.5 + - + +
119A GLY* 1.3 72.5 - - - -
121A TYR* 1.3 61.3 - - - +
136A ASP* 4.9 8.2 - - + +
137A ILE 3.4 3.5 + - - +
138A TRP* 3.4 17.0 + - - +
1C NAG 1.4 71.5 + - - +
5C FUC 3.1 12.3 - - + +
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Residues in contact with TYR 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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47A LEU* 4.7 9.9 - - + -
66A TRP* 4.3 16.8 - + + -
67A ALA 3.4 9.4 - - - +
68A ARG* 3.2 43.1 + - + -
75A MET* 3.7 32.5 - - + -
110A MET* 4.4 7.8 - - - -
117A ASP* 2.6 39.6 + - - +
119A GLY 3.3 21.5 - - - -
120A ASN* 1.3 75.3 - - - +
122A THR* 1.3 61.5 + - - +
123A CYS 4.0 0.2 + - - -
135A VAL 3.9 0.3 - - - +
136A ASP* 3.5 2.1 - - - -
137A ILE* 2.7 46.2 + - + +
139A LEU* 3.8 22.0 - - + +
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Residues in contact with THR 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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65A THR 3.9 0.9 + - - +
66A TRP* 3.4 7.6 - - - -
67A ALA* 2.9 46.8 + - + +
68A ARG 4.6 5.4 - - - +
69A HIS* 3.6 23.6 - - + +
70A GLY 5.8 0.4 - - - +
121A TYR* 1.3 73.7 - - - +
123A CYS* 1.3 64.2 + - - +
124A LEU* 4.7 5.9 + - - +
134A SER* 5.1 8.0 - - - -
135A VAL 3.4 6.7 - - - -
136A ASP* 3.2 20.6 - - - +
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Residues in contact with CYS 123 (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 VAL* 4.7 1.0 - - - +
49A CYS* 2.0 48.2 - - - -
65A THR 3.6 5.8 - - - -
66A TRP* 3.8 25.4 - - + -
106A ALA* 3.7 16.8 - - - -
121A TYR 4.0 0.4 + - - -
122A THR* 1.3 74.0 - - - +
124A LEU* 1.3 62.2 + - - +
125A PHE* 4.1 7.2 - - - -
133A ARG 4.2 0.3 - - - +
134A SER* 3.2 2.1 - - - -
135A VAL* 2.9 29.8 + - + +
137A ILE* 4.0 5.4 - - + -
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Residues in contact with LEU 124 (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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64A LEU* 3.4 5.0 - - - +
65A THR* 2.9 51.8 + - + +
122A THR* 4.1 6.0 + - - +
123A CYS* 1.3 73.9 - - - +
125A PHE* 1.3 78.4 + - - +
126A VAL* 3.4 24.0 - - + -
132A SER* 4.1 13.0 - - - +
133A ARG 3.4 5.4 - - - +
134A SER* 3.0 26.2 - - - +
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Residues in contact with PHE 125 (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 VAL* 3.8 30.3 - - + -
49A CYS* 3.9 7.6 - - - -
50A TYR 4.2 1.8 - - - -
51A LEU* 3.9 27.6 - - + -
61A VAL* 3.8 19.7 - - + -
63A GLN 3.8 2.5 - - - -
64A LEU* 4.2 17.9 - - + -
103A LEU 4.5 2.0 - - - -
104A ARG* 3.2 38.8 - - - -
106A ALA* 3.5 26.0 - - + -
123A CYS* 4.5 0.7 - - - -
124A LEU* 1.3 82.2 - - - +
126A VAL* 1.3 59.2 + - - +
127A THR* 3.7 15.7 + - + -
132A SER* 3.2 27.7 - - - -
133A ARG* 2.9 13.8 + - - +
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Residues in contact with VAL 126 (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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61A VAL* 4.2 1.3 - - - -
62A SER* 2.7 44.7 + - - +
63A GLN* 2.9 42.6 + - + +
65A THR* 4.9 2.5 - - - +
124A LEU* 3.4 23.1 - - + -
125A PHE* 1.3 71.1 - - - +
127A THR* 1.3 62.5 + - - +
131A GLY 4.2 1.8 - - - +
132A SER* 4.3 8.7 - - - -
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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