Contacts of the strand formed by residues 128 - 138 (chain A) in PDB entry 1Q1C
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 LEU 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A TRP 3.8 3.1 - - - +
61A LEU* 3.7 13.9 - - + -
67A PHE* 3.9 14.1 - - + -
105A ILE 3.6 0.9 - - - +
106A THR* 3.1 4.0 - - - +
107A CYS* 2.6 45.2 + - + +
112A ALA* 4.0 10.1 - - + -
113A TYR* 3.9 30.5 - - + -
122A ILE* 3.6 25.8 - - + -
126A ALA* 4.0 13.7 - - + +
127A THR* 1.3 80.0 - - - +
129A VAL* 1.3 63.5 + - - +
130A PHE* 3.7 35.7 - - + -
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Residues in contact with VAL 129 (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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59A GLY* 3.4 2.9 - - - -
60A TRP* 2.9 59.6 + - + +
61A LEU 4.7 3.8 - - - +
62A LEU* 3.8 24.5 - - + -
104A HIS* 4.9 10.1 - - + -
105A ILE 3.2 8.3 - - - +
106A THR* 3.4 21.8 - - + +
128A LEU* 1.3 77.0 - - - +
130A PHE* 1.3 70.5 + - - +
303A DMS 4.3 12.8 - - + +
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Residues in contact with PHE 130 (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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57A TYR* 4.2 9.6 - + - -
58A THR 3.3 5.6 - - - +
59A GLY* 3.7 21.3 - - - -
60A TRP* 4.5 1.6 - - - -
67A PHE* 4.0 12.3 - + - -
87A ILE* 3.7 19.7 - - + -
90A TRP* 3.5 38.1 - + - +
103A CYS 3.7 0.2 - - - +
104A HIS* 3.1 7.9 - - - +
105A ILE* 2.8 44.2 + - + +
107A CYS* 3.9 15.0 - - - -
113A TYR* 5.4 2.7 - + - -
128A LEU* 3.7 35.7 - - + -
129A VAL* 1.3 78.3 - - - +
131A GLU* 1.3 60.1 + - - +
132A VAL* 3.9 12.5 + - + -
301A DMS 4.3 10.1 - - + -
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Residues in contact with GLU 131 (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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38A LYS* 3.4 19.1 - - - -
56A HIS 3.8 0.3 - - - +
57A TYR* 3.1 27.7 - - - +
58A THR* 3.0 17.1 + - - +
60A TRP* 3.8 22.3 - - + -
71A LEU* 5.2 6.2 - - - +
102A VAL* 4.3 13.6 - - + +
103A CYS 3.3 5.6 - - - +
104A HIS* 2.8 33.4 + - + +
130A PHE* 1.3 73.8 - - - +
132A VAL* 1.3 63.3 + - - +
133A GLU 5.5 0.2 - - - +
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Residues in contact with VAL 132 (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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55A VAL* 4.0 29.4 - - + -
56A HIS 3.7 3.6 - - - +
57A TYR* 4.6 1.1 - - + -
90A TRP* 4.5 14.4 - - + -
93A ALA* 6.2 0.4 - - + -
94A ILE* 4.3 11.9 - - + -
97A MET* 3.2 30.0 - - + +
102A VAL* 3.3 2.8 - - - -
103A CYS* 2.8 42.4 + - - +
105A ILE* 4.4 15.5 - - + -
130A PHE* 4.1 20.9 - - + +
131A GLU* 1.3 79.4 - - - +
133A GLU* 1.3 62.1 + - - +
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Residues in contact with GLU 133 (chain A).
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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39A ARG* 2.9 29.7 + - - +
55A VAL* 3.2 26.4 - - - +
56A HIS* 3.1 16.4 + - + +
100A GLY* 5.1 1.2 - - - -
101A GLU 3.2 10.5 - - - +
102A VAL* 3.8 16.0 - - + +
131A GLU* 6.3 0.2 - - + -
132A VAL* 1.3 75.3 - - - +
134A LEU* 1.3 67.1 + - - +
135A PHE* 3.3 41.0 + - + -
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Residues in contact with LEU 134 (chain A).
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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47A PRO* 4.0 16.6 - - + -
53A VAL* 4.2 14.6 - - + -
54A PHE 3.6 16.2 - - - +
55A VAL* 3.8 13.5 - - + -
94A ILE* 4.5 6.7 - - + +
97A MET* 3.7 36.3 - - + +
98A LYS 3.7 29.6 - - - +
99A VAL* 4.0 5.6 - - - +
100A GLY* 2.9 27.0 + - - -
101A GLU 3.0 8.3 + - - -
133A GLU* 1.3 71.9 - - - +
135A PHE* 1.3 58.0 + - - +
136A GLU 3.8 17.7 - - - +
137A PHE* 4.3 7.6 - - + -
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Residues in contact with PHE 135 (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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54A PHE* 2.8 15.5 + - + +
55A VAL* 3.9 4.3 - - - -
56A HIS* 3.5 44.9 - + + -
76A LYS* 3.5 38.6 - - + -
99A VAL* 3.2 18.5 - - - +
100A GLY* 5.0 1.1 - - - +
133A GLU* 3.3 45.5 - - + -
134A LEU* 1.3 73.7 - - - +
136A GLU* 1.3 65.0 + - + +
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Residues in contact with GLU 136 (chain A).
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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53A VAL* 3.6 0.5 - - - -
54A PHE* 2.9 57.4 + - + +
99A VAL* 4.5 8.1 - - - -
134A LEU* 3.7 6.0 - - - +
135A PHE* 1.3 85.5 - - + +
137A PHE* 1.3 76.9 + - - +
138A LYS* 4.1 15.2 + - - +
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Residues in contact with PHE 137 (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 GLU* 3.9 28.7 - - + -
46A MET 3.7 6.7 - - - -
47A PRO* 3.6 46.0 - - + -
51A ASP* 3.8 10.3 - - + -
52A ARG 3.1 13.9 - - - +
53A VAL* 3.9 15.5 - - + -
54A PHE* 4.5 0.9 - - - -
99A VAL* 3.6 29.6 - - + +
134A LEU* 4.3 6.7 - - + -
136A GLU* 1.3 85.9 - - - +
138A LYS* 1.3 68.2 + - - +
153A ARG* 3.7 26.7 + - - -
305A DMS 5.4 0.7 - - - +
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Residues in contact with LYS 138 (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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51A ASP* 3.3 9.3 - - - -
52A ARG* 2.8 52.8 + - + +
54A PHE* 4.1 22.2 - - + -
136A GLU* 4.1 16.6 + - - +
137A PHE* 1.3 78.9 - - - +
139A GLY* 1.3 71.1 + - - +
153A ARG* 4.4 0.7 - - - -
305A DMS 4.2 12.6 - - + -
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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