Contacts of the strand formed by residues 1102 - 1108 (chain B) in PDB entry 1W21
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 SER1102 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100B VAL* 3.6 4.3 - - - +
1101B ASN* 1.3 77.6 - - - +
1103B TRP* 1.3 68.7 + - - +
1368B TRP* 4.5 2.2 - - - -
1401B GLN* 3.7 11.9 - - - -
1456B GLY* 3.6 4.3 - - - -
1457B SER* 2.9 26.9 + - - +
1459B LYS 2.6 22.0 + - - -
1460B ARG* 4.4 1.8 - - - -
1461B LEU* 3.1 36.3 + - - +
2F NAG 4.5 7.4 - - - -
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Residues in contact with TRP1103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100B VAL* 3.7 13.7 - - + -
1102B SER* 1.3 78.7 - - - +
1104B HIS* 1.3 60.2 + - - +
1105B ILE 4.4 0.2 + - - -
1361B PHE* 4.2 13.5 - + - -
1368B TRP* 3.3 47.3 - + + -
1383B MET* 3.6 37.8 - - + +
1401B GLN* 2.8 44.7 + - + +
1403B ILE* 4.6 0.9 - - + -
1428B PRO* 3.7 31.0 - - + -
1429B CYS 4.5 0.4 - - - -
1430B PHE* 3.6 28.5 - + + -
1454B LEU* 4.1 16.1 - - + +
1455B CYS* 3.3 8.7 - - - +
1456B GLY* 3.4 29.4 - - - -
1461B LEU* 4.3 10.1 - - - +
1462B GLY 5.0 2.6 - - - +
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Residues in contact with HIS1104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102B SER 4.4 0.2 + - - -
1103B TRP* 1.3 73.1 - - - +
1105B ILE* 1.3 86.6 + - - +
1106B LEU* 4.4 4.9 - - + -
1423B LYS* 5.7 1.6 + - - -
1427B ASN* 4.7 1.6 + - - -
1454B LEU* 3.1 6.4 - - - +
1455B CYS* 2.8 66.5 + - + +
1456B GLY 3.4 16.0 + - - -
1457B SER* 4.5 0.6 - - - -
1461B LEU* 3.5 24.0 - - + +
3209D SER* 5.9 0.7 - - - +
3211D VAL* 3.9 15.0 - - + +
3218D PRO* 3.7 35.0 - - + +
3221D GLU* 3.9 25.6 + - + -
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Residues in contact with ILE1105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1104B HIS* 1.3 87.4 + - - +
1106B LEU* 1.3 58.0 + - - +
1107B SER 3.8 7.0 - - - +
1108B LYS* 4.9 0.2 - - + -
1452B VAL* 3.8 16.4 - - + -
1453B ALA 3.5 18.2 - - - +
1454B LEU* 4.1 6.7 - - + +
1466B TRP* 3.6 44.2 - - + +
3183D ILE* 3.6 39.9 + - + +
3202D SER* 4.0 18.8 - - - +
3211D VAL* 4.0 17.1 - - + +
3213D TRP* 4.4 5.4 + - - -
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Residues in contact with LEU1106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1104B HIS* 3.5 2.6 + - + -
1105B ILE* 1.3 73.9 - - - +
1107B SER* 1.4 59.2 + - - +
1135B CYS* 5.5 3.8 - - - -
1169B MET* 3.9 21.7 - - + +
1416B PHE* 3.6 35.4 - - + -
1429B CYS* 4.6 0.4 - - - -
1453B ALA* 2.8 23.6 + - + +
1454B LEU* 4.1 1.1 - - - -
1455B CYS* 3.7 23.8 - - - +
3180D VAL* 5.9 0.9 - - - +
3182D CYS* 5.2 0.7 - - - -
3183D ILE* 3.8 9.1 + - - +
3213D TRP* 3.2 48.4 - - + -
3218D PRO* 3.8 26.7 - - + -
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Residues in contact with SER1107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1105B ILE* 3.8 1.4 - - - +
1106B LEU* 1.4 83.1 - - - +
1108B LYS* 1.3 67.5 + - - +
1137B MET* 3.4 9.7 - - - +
1169B MET* 3.4 25.1 - - - +
1170B GLY* 3.3 30.7 + - - -
1452B VAL* 3.5 2.8 - - - +
1453B ALA* 2.7 35.8 + - - +
3180D VAL* 5.2 1.4 - - - +
3183D ILE* 3.6 12.8 - - - +
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Residues in contact with LYS1108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1105B ILE* 4.9 1.1 - - + -
1107B SER* 1.3 82.5 + - - +
1109B ASP* 1.3 60.5 + - - +
1110B ASN* 2.7 40.3 + - - +
1137B MET* 4.6 1.1 - - - -
1170B GLY* 3.7 8.8 - - - +
1434B LEU* 4.5 4.5 - - - +
1450B SER* 4.6 1.4 + - - -
1451B ILE 3.3 17.9 - - - +
1452B VAL* 4.1 7.9 - - + -
1466B TRP* 3.6 29.2 - - + +
1467B HIS 3.0 29.4 + - - -
1468B ASP* 3.1 13.7 + - - +
3160D PRO 3.2 26.0 - - - +
3161D PHE* 3.9 3.5 - - - -
3180D VAL* 5.4 1.2 - - - +
3183D ILE* 3.6 26.2 - - + +
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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