Contacts of the strand formed by residues 124 - 132 (chain A) in PDB entry 3PE7
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 TRP 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A VAL* 3.7 15.9 - - + +
121A PRO* 3.1 28.0 + - + +
122A ALA 3.2 0.6 - - - -
123A GLU* 1.3 98.8 - - + +
125A VAL* 1.3 68.6 + - - +
143A GLU* 3.7 19.5 - - + +
144A ILE 3.3 9.2 - - - -
145A ARG* 3.3 66.7 - - - +
146A ARG* 3.8 11.7 + - - +
167A CYS* 3.9 13.0 - - - -
169A ARG* 3.5 62.7 - - + +
185A GLN* 3.8 12.8 - - - -
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Residues in contact with VAL 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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101A GLY 5.8 1.1 - - - +
120A VAL* 4.1 3.1 - - - -
124A TRP* 1.3 79.2 - - - +
126A GLY* 1.3 77.9 + - - +
127A TYR* 3.4 0.3 + - - +
143A GLU* 3.4 1.0 - - - -
144A ILE* 2.8 39.4 + - + +
146A ARG* 4.0 31.4 - - + +
149A TRP* 3.7 53.4 - - + +
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Residues in contact with GLY 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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101A GLY 4.4 14.6 + - - +
120A VAL* 3.8 25.7 - - - +
125A VAL* 1.3 84.9 - - - +
127A TYR* 1.3 58.1 + - - +
128A GLY 4.3 1.6 - - - -
130A TRP* 5.1 7.6 - - - -
142A ILE 3.6 8.3 - - - -
143A GLU* 4.5 1.8 - - - -
149A TRP* 5.3 3.8 - - - -
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Residues in contact with TYR 127 (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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125A VAL 3.4 0.4 + - - +
126A GLY* 1.3 72.8 - - - +
128A GLY* 1.3 77.6 + - - +
129A THR 3.9 1.2 + - - +
130A TRP* 5.6 1.6 + - - +
142A ILE* 2.9 40.0 + - + +
144A ILE* 3.7 25.4 - - + -
149A TRP* 3.8 24.2 - + + -
152A LEU* 4.2 11.0 - - + -
158A PHE* 3.8 13.2 - + - -
189A TRP* 3.4 41.1 + + - -
190A LEU 3.9 18.8 - - - -
191A GLY* 4.2 11.4 - - - -
192A HIS 5.1 1.8 - - - -
193A PRO* 5.8 0.7 - - - +
208A GLU* 3.8 10.2 + - + +
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Residues in contact with GLY 128 (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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82A ASN* 5.6 4.0 + - - -
98A VAL* 5.7 1.7 - - - +
126A GLY 5.3 0.9 - - - -
127A TYR* 1.3 93.8 + - - +
129A THR* 1.3 62.9 + - - -
130A TRP* 4.1 10.2 + - - -
192A HIS 6.3 0.9 - - - -
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Residues in contact with THR 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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37A TYR* 3.3 21.8 - - + -
39A TYR* 3.3 29.0 + - + +
40A GLN* 3.3 30.3 - - + +
85A GLY* 3.7 21.5 - - - +
127A TYR 3.9 0.9 + - - +
128A GLY* 1.3 73.5 - - - -
130A TRP* 1.3 67.3 + - - +
131A VAL* 3.8 7.8 + - + +
140A VAL 4.0 4.2 - - - +
141A GLY* 4.4 6.9 - - - -
192A HIS* 5.8 2.3 - - - +
193A PRO* 4.6 11.2 - - - +
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Residues in contact with TRP 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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40A GLN* 3.1 18.7 - - - +
85A GLY 4.4 1.2 - - - +
87A PHE* 3.9 10.4 - - + -
98A VAL* 3.7 29.2 - - + +
101A GLY 5.9 0.8 + - - -
104A LEU* 4.2 14.7 - - + +
118A TYR* 3.9 13.9 - + - -
120A VAL* 4.1 19.1 - - + +
126A GLY* 5.1 7.6 - - - -
127A TYR 5.6 1.6 + - - +
128A GLY 4.4 8.7 + - - -
129A THR* 1.3 76.7 - - - +
131A VAL* 1.3 60.1 + - - +
139A LEU* 4.1 30.5 - - + -
140A VAL* 3.3 9.4 - - - -
141A GLY* 3.5 34.1 - - - -
142A ILE 4.6 5.1 + - - -
143A GLU* 3.7 31.0 - - + -
171A MET* 4.1 15.7 - - + -
173A VAL* 3.7 20.0 - - + -
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Residues in contact with VAL 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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39A TYR* 3.9 22.9 - - + -
40A GLN* 4.1 12.8 - - - +
129A THR* 4.1 7.0 - - + +
130A TRP* 1.3 79.5 - - - +
132A ALA* 1.3 74.1 + - - +
139A LEU* 3.3 4.0 - - - -
140A VAL* 2.9 34.9 + - + +
192A HIS* 5.6 1.1 - - + -
193A PRO 3.7 21.5 - - - +
194A ILE* 3.8 31.2 - - + -
195A TYR* 4.0 6.0 - - + +
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Residues in contact with ALA 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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40A GLN* 5.1 2.2 - - - +
87A PHE* 3.7 24.5 - - + -
131A VAL* 1.3 89.0 - - - +
133A ASN* 1.3 71.8 + - - +
136A CYS* 4.3 13.2 - - - -
138A LYS 3.3 11.9 - - - +
139A LEU* 3.7 14.8 - - + +
195A TYR* 3.9 7.7 - - - +
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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