Contacts of the strand formed by residues 313 - 320 (chain C) in PDB entry 3STJ
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 LYS 313 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291C ASN* 4.6 2.3 + - - +
312C THR* 1.3 79.2 - - - +
314C VAL* 1.3 64.1 + - - +
328C GLU* 3.6 35.1 + - + +
329C VAL 3.2 6.1 - - - +
330C THR* 3.4 30.0 + - + +
72I ALA 4.7 2.7 - - - +
73I SER* 3.2 49.2 + - - +
121I PRO* 2.6 39.6 + - - +
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Residues in contact with VAL 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C LEU* 4.1 5.6 - - + -
290C LEU* 3.7 20.2 - - + -
291C ASN* 3.5 15.0 - - - +
305C ILE* 4.2 3.8 - - + -
308C THR* 4.6 13.7 - - + +
312C THR* 4.7 2.0 - - + +
313C LYS* 1.3 77.5 - - - +
315C LYS* 1.3 60.1 + - - +
316C LEU* 3.8 21.5 - - + -
327C VAL 3.5 1.2 - - - +
328C GLU* 3.2 5.1 - - - -
329C VAL* 2.8 42.0 + - + +
331C LEU* 4.0 35.7 - - + -
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Residues in contact with LYS 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C LEU* 3.4 7.1 - - - +
291C ASN* 2.7 48.4 + - - +
292C GLY 5.2 0.2 - - - +
314C VAL* 1.3 75.5 - - - +
316C LEU* 1.3 59.7 + - - +
317C GLY 4.0 0.7 + - - -
326C GLU* 3.4 31.1 - - - +
327C VAL 3.5 2.9 - - - +
328C GLU* 3.5 31.6 - - + +
123I LYS* 4.1 31.0 + - - +
124I LEU 4.6 7.2 + - - -
125I THR* 5.8 1.2 + - - -
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Residues in contact with LEU 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C LEU* 4.1 18.8 - - + -
244C ILE* 5.7 0.2 - - + -
276C SER* 5.0 0.9 - - - +
281C VAL* 4.2 14.4 - - + -
287C ILE* 3.9 40.4 - - + -
289C SER 3.6 2.2 - - - +
290C LEU* 3.9 15.5 - - + -
301C LEU* 5.0 1.3 - - + -
305C ILE* 4.9 0.2 - - + -
314C VAL* 3.8 27.6 - - + -
315C LYS* 1.3 71.3 - - - +
317C GLY* 1.3 61.2 + - - +
318C LEU* 3.3 10.1 + - + +
325C LEU 3.6 0.2 - - - +
326C GLU* 3.4 7.5 - - - -
327C VAL* 2.7 39.8 + - + +
329C VAL* 3.8 20.9 - - + -
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Residues in contact with GLY 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C ILE* 3.2 7.3 - - - +
288C THR* 2.6 35.3 + - - -
289C SER* 2.9 30.6 + - - -
316C LEU* 1.3 67.2 - - - +
318C LEU* 1.3 56.2 + - - -
325C LEU 3.9 4.5 - - - -
326C GLU* 3.9 11.9 + - - -
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Residues in contact with LEU 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281C VAL* 4.3 16.2 - - + -
285C ASP* 3.4 43.5 - - + +
286C ILE 3.5 7.2 - - - +
287C ILE* 4.5 7.0 - - + +
288C THR* 4.9 2.7 + - - -
316C LEU* 3.9 12.3 - - + +
317C GLY* 1.3 73.8 - - - -
319C LEU* 1.3 76.6 + - - +
320C ARG* 4.1 7.6 - - - +
324C PRO* 3.6 5.9 - - - +
325C LEU* 2.9 62.2 + - + +
327C VAL* 4.2 21.3 - - + -
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Residues in contact with LEU 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C LEU* 4.0 31.0 - - + -
260C ASP 5.6 1.1 - - - +
261C VAL* 3.8 27.1 - - + -
284C GLY 4.4 1.6 - - - +
285C ASP* 3.9 1.7 - - - -
286C ILE* 3.1 43.5 + - + +
288C THR* 4.5 7.6 - - + +
318C LEU* 1.3 84.6 - - - +
320C ARG* 1.4 60.7 + - - +
321C ASN 4.2 0.9 + - - -
322C GLY* 4.2 14.7 + - - +
323C LYS 3.5 4.7 - - - +
324C PRO* 3.8 27.4 - - + -
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Residues in contact with ARG 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C GLY 2.5 31.1 + - - -
281C VAL* 4.0 0.8 - - - +
282C LYS* 3.4 41.2 - - - +
284C GLY 5.4 2.2 - - - +
285C ASP* 3.0 41.5 + - - +
318C LEU* 4.2 8.4 - - + +
319C LEU* 1.4 70.2 - - - +
321C ASN* 1.3 73.8 + - + +
322C GLY 3.1 0.7 - - - -
323C LYS* 3.0 31.5 + - + +
325C LEU* 3.6 31.8 - - + +
327C VAL* 5.2 3.4 - - - +
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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