Contacts of the strand formed by residues 1113 - 1118 (chain A) in PDB entry 3M5M
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 VAL1113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1000A LEU* 4.6 4.0 - - + -
1005A ALA* 3.9 26.5 - - + -
1105A TYR* 3.8 34.2 - - + -
1106A LEU 3.3 3.6 - - - +
1107A VAL* 4.5 16.2 - - + -
1111A ALA 3.9 0.4 + - - +
1112A ASP* 1.3 88.0 + - - +
1114A ILE* 1.3 60.5 + - - +
1115A PRO* 3.8 7.3 - - - +
1130A ARG* 4.7 2.4 + - - -
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Residues in contact with ILE1114 (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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1105A TYR* 3.5 2.6 - - - -
1106A LEU* 2.8 42.7 + - + +
1108A THR* 3.6 28.7 - - + -
1112A ASP* 3.7 18.4 - - + +
1113A VAL* 1.3 76.7 - - - +
1115A PRO* 1.3 71.8 - - + +
1116A VAL* 3.5 2.8 + - - +
1126A LEU* 3.4 27.1 - - + -
1128A SER* 3.9 17.3 - - - +
1130A ARG* 3.8 32.1 - - + +
1134A TYR* 6.4 0.2 - - + -
1135A LEU* 3.9 12.8 - - + -
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Residues in contact with PRO1115 (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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1104A LEU 3.6 7.6 - - - +
1105A TYR* 4.1 22.0 - - + -
1113A VAL 3.8 8.1 - - - +
1114A ILE* 1.3 94.3 - - + +
1116A VAL* 1.3 62.1 + - - +
1126A LEU* 3.8 0.2 - - - -
1127A LEU* 3.1 44.1 + - + -
1128A SER* 4.2 12.1 + - - -
1130A ARG* 5.2 2.5 - - - +
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Residues in contact with VAL1116 (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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1103A ASP* 3.9 1.0 - - - -
1104A LEU* 2.8 51.8 + - + +
1106A LEU* 4.0 15.0 - - + +
1114A ILE 3.5 9.4 - - - +
1115A PRO* 1.3 77.5 - - - +
1117A ARG* 1.3 63.4 + - - +
1118A ARG 4.6 0.2 - - - +
1124A GLY* 3.7 25.8 - - - -
1125A SER 3.2 11.9 - - - +
1126A LEU* 3.4 27.6 - - + -
1127A LEU* 4.1 4.4 - - - +
1143A LEU* 4.3 10.1 - - + -
1167A VAL* 3.9 12.6 - - + -
1169A PHE* 5.8 0.2 - - + -
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Residues in contact with ARG1117 (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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1102A SER* 3.5 31.6 + - - +
1103A ASP* 2.9 33.8 + - - +
1116A VAL* 1.3 72.4 - - - +
1118A ARG* 1.3 71.4 + - - +
1119A ARG* 3.5 30.1 + - - +
1124A GLY* 4.0 1.1 - - - -
1125A SER* 2.8 39.8 + - - +
1127A LEU* 3.6 26.4 - - + +
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Residues in contact with ARG1118 (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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1101A SER 4.5 9.5 + - - -
1102A SER* 2.8 40.6 + - - +
1104A LEU* 3.9 15.4 - - + +
1116A VAL 3.8 1.4 + - - -
1117A ARG* 1.3 86.3 + - - +
1119A ARG* 1.3 64.0 + - - +
1120A GLY 2.9 25.0 + - - +
1121A ASP* 2.7 29.2 + - - +
1123A ARG 3.7 7.9 - - - +
1124A GLY* 4.0 2.9 - - - -
1151A VAL* 3.7 18.8 - - - +
1169A PHE* 3.6 19.0 - - + -
1171A PRO* 3.8 16.2 - - - +
1173A GLU* 4.4 10.1 + - - -
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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