Contacts of the strand formed by residues 130 - 141 (chain A) in PDB entry 2P7I
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 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A ARG* 4.1 11.7 - - - -
103A TYR 3.9 2.5 - - - +
106A ILE* 3.7 16.1 - - + +
125A ILE* 3.0 25.5 + - + +
126A ASN* 4.4 6.9 + - - +
127A ASP 5.8 0.3 - - - +
128A ASP 4.8 0.5 - - - -
129A TRP* 1.3 77.2 + - - +
131A ALA* 1.3 65.2 + - - +
132A GLU 3.9 0.5 + - - -
134A GLY* 3.6 8.5 - - - +
135A ARG 3.6 39.9 - - - +
136A LEU* 4.0 4.9 - - + +
190A LEU* 4.0 17.9 - - + -
244A GLU* 4.0 6.7 - - - -
245A LYS* 3.6 47.1 + - + +
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Residues in contact with ALA 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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102A ARG* 4.0 7.9 - - + +
103A TYR 2.9 34.4 + - - +
104A ASP* 4.0 13.7 - - - +
129A TRP 3.5 2.4 + - - -
130A LEU* 1.3 79.3 - - - +
132A GLU* 1.3 66.5 + - - +
133A GLY 3.3 0.3 + - - -
134A GLY* 2.8 20.2 + - - +
245A LYS* 4.7 5.2 - - - +
250A CL 3.5 15.0 - - + -
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Residues in contact with GLU 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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41A ARG* 4.7 3.8 + - - -
104A ASP* 4.9 2.6 - - - +
130A LEU 3.9 0.4 + - - -
131A ALA* 1.3 78.7 - - - +
133A GLY* 1.3 60.3 + - - +
134A GLY 3.3 1.7 + - - -
245A LYS* 2.6 41.4 + - - +
250A CL 3.2 19.3 - - + +
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Residues in contact with GLY 133 (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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41A ARG* 2.9 38.8 + - - -
104A ASP* 5.6 0.7 - - - -
131A ALA 3.3 0.4 + - - -
132A GLU* 1.3 72.7 + - - +
134A GLY* 1.3 63.7 + - - +
135A ARG* 4.3 3.1 + - - +
244A GLU* 4.8 9.9 - - - +
245A LYS* 5.6 3.0 - - - +
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Residues in contact with GLY 134 (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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41A ARG* 4.8 0.2 - - - -
103A TYR 3.9 6.1 - - - -
104A ASP* 3.2 22.9 + - - -
130A LEU* 3.6 8.8 - - - +
131A ALA* 2.8 17.5 + - - +
132A GLU 3.1 2.6 + - - -
133A GLY* 1.3 81.5 - - - +
135A ARG* 1.3 62.1 + - - +
244A GLU* 3.7 21.1 - - - +
245A LYS 4.3 2.8 + - - -
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Residues in contact with ARG 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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38A PRO 4.8 0.2 + - - -
39A PHE* 2.7 42.8 + - - +
40A PHE 4.5 2.0 + - - -
41A ARG* 3.7 29.4 - - + +
104A ASP 2.9 8.5 + - - +
105A ASN* 3.3 3.5 - - - -
106A ILE 2.8 30.8 + - - +
130A LEU* 3.6 6.6 - - - +
133A GLY 4.3 2.1 + - - +
134A GLY* 1.3 78.6 - - - +
136A LEU* 1.3 54.2 + - - +
137A PHE* 3.7 17.3 - - + -
242A LEU* 4.1 19.4 - - + +
243A CYS 3.3 5.4 - - - +
244A GLU* 4.2 24.7 + - + -
37B THR* 4.6 3.6 + - - +
38B PRO* 3.0 46.3 + - - +
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Residues in contact with LEU 136 (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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106A ILE* 3.4 35.7 - - + +
108A LEU* 4.2 15.5 - - + -
122A LEU* 4.2 12.8 - - + -
125A ILE* 4.1 27.4 - - + -
130A LEU* 4.0 7.0 - - + +
135A ARG* 1.3 72.1 - - - +
137A PHE* 1.3 63.0 + - - +
138A LEU* 4.2 20.0 - - + -
190A LEU* 3.8 28.9 - - + -
241A LEU 3.4 5.2 - - - +
242A LEU* 3.4 4.9 - - - +
243A CYS* 2.8 47.4 + - + +
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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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36A PHE* 3.4 58.8 - + + -
39A PHE* 3.6 24.9 - - + -
40A PHE* 3.6 17.9 - + - -
105A ASN* 3.5 23.8 - - + -
106A ILE 2.8 23.0 + - - +
107A VAL* 3.8 8.5 - - + -
108A LEU 3.0 28.2 + - - +
109A THR* 4.1 2.8 - - - +
135A ARG* 3.7 18.6 - - + -
136A LEU* 1.3 73.2 - - - +
138A LEU* 1.3 60.6 + - - +
139A VAL* 3.9 2.4 + - - -
240A PHE* 3.9 6.1 - + - -
241A LEU 4.1 2.5 - - - -
242A LEU* 3.6 23.3 - - + -
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Residues in contact with LEU 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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108A LEU* 3.6 33.0 - - + +
112A LEU* 4.0 18.2 - - + -
122A LEU* 4.2 18.6 - - + -
136A LEU* 4.2 16.2 - - + -
137A PHE* 1.3 70.5 - - - +
139A VAL* 1.3 62.8 + - - +
140A CYS* 4.5 2.9 - - - -
181A LEU* 3.8 32.0 - - + +
185A ALA* 4.3 19.5 - - + -
239A ILE 3.8 0.7 - - - +
240A PHE* 3.3 4.2 - - - -
241A LEU* 2.8 51.5 + - + +
243A CYS* 4.6 1.3 - - - -
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Residues in contact with VAL 139 (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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32A MSE 4.1 11.4 - - + -
36A PHE* 3.5 37.7 - - + -
108A LEU 3.2 7.8 + - - +
109A THR* 3.5 12.3 - - + -
110A HIS* 2.8 39.2 + - + +
111A VAL 4.6 0.2 + - - -
138A LEU* 1.3 82.2 - - - +
140A CYS* 1.3 66.1 + - - +
198A ILE* 4.2 9.4 - - + -
238A SER* 3.6 22.7 - - - -
239A ILE 3.2 9.6 - - - +
240A PHE* 3.8 13.0 - - + -
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Residues in contact with CYS 140 (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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110A HIS* 3.9 6.7 - - - -
112A LEU* 4.0 14.8 - - - -
113A GLU* 3.4 16.8 - - + +
138A LEU* 4.5 3.8 - - - -
139A VAL* 1.3 78.9 - - - +
141A PRO* 1.3 81.8 - - + +
176A TYR* 3.7 32.8 - - + -
181A LEU* 3.9 22.6 - - + +
238A SER* 3.3 0.9 - - - -
239A ILE* 3.0 28.7 + - + +
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Residues in contact with PRO 141 (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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110A HIS* 3.7 20.8 - - + +
113A GLU* 3.2 35.4 - - + +
140A CYS* 1.3 94.0 - - + +
142A ASN* 1.3 60.9 + - - +
143A ALA 3.8 0.2 + - - -
172A HIS* 4.6 13.7 - - + -
175A THR* 4.8 6.7 - - + +
176A TYR 3.4 17.5 + - - +
237A ALA 3.6 9.2 - - - +
238A SER* 3.9 5.4 - - - +
239A ILE* 4.6 0.3 - - - +
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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