Contacts of the strand formed by residues 1025 - 1035 (chain I) in PDB entry 3F5P
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 GLU1025 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1020I GLY* 3.9 7.6 - - - -
1022I VAL* 3.2 39.7 + - + +
1023I LYS 3.1 5.0 - - - +
1024I ASP* 1.3 85.7 - - - +
1026I PRO* 1.3 71.1 - - - +
1027I GLU* 3.2 15.7 + - - +
1028I THR* 3.7 26.3 + - - +
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Residues in contact with PRO1026 (chain I).
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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1019I LYS* 3.4 5.7 - - - +
1020I GLY* 2.5 32.4 + - - +
1024I ASP 4.1 5.2 - - - +
1025I GLU* 1.3 83.1 - - - +
1027I GLU* 1.3 64.4 + - + +
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Residues in contact with GLU1027 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017I VAL* 3.8 22.2 - - + +
1018I ALA 3.7 4.7 - - - -
1019I LYS* 3.0 38.9 - - + +
1025I GLU* 3.4 16.1 - - - +
1026I PRO* 1.3 88.0 - - + +
1028I THR* 1.3 68.1 + - - +
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Residues in contact with THR1028 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017I VAL* 3.3 7.0 - - - +
1018I ALA 2.9 37.0 + - - -
1021I VAL* 4.4 0.9 - - - -
1022I VAL* 3.0 42.6 + - + +
1025I GLU* 3.7 16.4 + - - +
1027I GLU* 1.3 81.4 + - - +
1029I ARG* 1.3 77.4 + - - +
1030I VAL* 3.6 9.6 - - + +
1066I LEU* 4.8 3.1 - - + -
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Residues in contact with ARG1029 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003I ARG* 5.4 1.8 - - - +
1015I GLU* 2.6 35.9 + - - -
1016I GLY 3.5 7.4 - - - +
1017I VAL* 4.7 8.3 - - + +
1028I THR* 1.3 82.8 - - - +
1030I VAL* 1.3 64.0 + - - +
1080I GLU* 4.9 0.9 - - - -
1081I LEU* 3.5 35.2 + - + +
1083I THR* 3.7 20.2 - - - +
1145I GLU* 3.8 15.6 + - - +
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Residues in contact with VAL1030 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1015I GLU* 3.6 2.6 - - - -
1016I GLY 2.8 44.8 + - - +
1018I ALA* 3.8 18.8 - - + +
1021I VAL* 4.8 0.2 - - + -
1028I THR* 3.6 12.6 - - - +
1029I ARG* 1.3 81.2 - - - +
1031I ALA* 1.3 59.5 + - - +
1032I ILE* 3.3 27.6 - - + -
1066I LEU* 3.5 26.9 - - + -
1078I ILE* 3.7 15.5 - - + -
1079I MET 3.5 8.7 - - - +
1081I LEU* 3.8 11.7 - - - +
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Residues in contact with ALA1031 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I 741 3.8 54.3 - - + +
1005I LEU* 4.6 3.1 - - + -
1013I VAL* 4.4 4.0 - - + -
1014I TYR 3.3 8.1 - - - +
1015I GLU* 4.6 1.1 - - - +
1030I VAL* 1.3 75.0 - - - +
1032I ILE* 1.3 63.2 + - - +
1077I VAL 3.6 1.2 - - - +
1078I ILE* 3.6 3.6 - - - -
1079I MET 2.9 33.8 + - - +
1081I LEU* 4.0 5.0 - - + +
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Residues in contact with ILE1032 (chain I).
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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9I 741 4.0 1.8 - - - -
999I ILE* 3.2 26.2 - - + -
1001I MET* 3.5 31.0 - - + -
1012I MET 3.7 0.9 - - - +
1013I VAL* 3.4 3.0 - - - -
1014I TYR* 2.7 48.4 + - + +
1015I GLU 4.4 2.0 - - - +
1016I GLY* 4.3 14.1 - - - +
1030I VAL* 3.3 30.3 - - + -
1031I ALA* 1.3 77.1 - - - +
1033I LYS* 1.3 62.2 + - - +
1034I THR 4.0 0.3 + - - -
1076I LEU* 4.1 20.2 - - + -
1077I VAL 3.5 1.1 - - - -
1078I ILE* 3.9 20.4 - - + -
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Residues in contact with LYS1033 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I 741 3.0 49.9 + - + +
1008I GLY* 3.7 3.6 - - - -
1009I SER* 2.7 37.7 + - - +
1010I PHE* 3.3 24.9 - - - +
1011I GLY 3.7 13.9 - - - +
1012I MET 3.5 2.5 - - - +
1013I VAL* 3.7 18.6 - - + +
1032I ILE* 1.3 73.6 - - - +
1034I THR* 1.3 63.6 + - - +
1035I VAL* 4.6 4.7 - - + +
1047I PHE* 4.1 15.9 - - + -
1075I THR 3.4 1.2 - - - +
1076I LEU* 3.2 9.2 - - - +
1077I VAL* 3.0 32.7 + - + +
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Residues in contact with THR1034 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001I MET* 3.5 26.5 - - + -
1011I GLY* 3.5 21.4 - - - -
1012I MET* 3.0 20.8 + - - +
1014I TYR* 3.9 13.0 - - + -
1032I ILE 4.0 0.2 + - - -
1033I LYS* 1.3 73.0 - - - +
1035I VAL* 1.3 62.9 + - - +
1036I ASN* 3.8 5.6 + - - +
1074I PRO* 4.4 13.7 - - + -
1075I THR 3.5 1.8 - - - -
1076I LEU* 3.3 27.1 - - + -
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Residues in contact with VAL1035 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010I PHE* 4.0 28.7 - - + +
1033I LYS* 4.6 2.7 - - + -
1034I THR* 1.3 75.0 - - - +
1036I ASN* 1.3 61.9 + - - +
1039I ALA* 3.9 24.5 - - + -
1043I GLU 5.9 0.7 - - - -
1044I ARG* 3.4 24.4 + - + +
1047I PHE* 3.1 48.2 - - + -
1074I PRO* 3.5 1.1 - - - +
1075I THR* 3.0 35.9 + - - +
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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